Even in the very worst days of early 1943, Allied Merchant Ship losses never exceeded 2% of Allied sailings
To put it one way according to the Bomber Command War Diaries some 3,775 Lancasters were lost during the war, or 2.36% of sorties, or to put it another way 56% of the 6,712 Lancasters officially built to the end of April 1945 were lost. One percentage figure tends to look more dramatic than the other.
Allied merchant ship losses of over 20,000,000 GRT can be compared with the merchant fleet strength of around 60,000,000 GRT at the end of the war or for more dramatic effect the smaller size in September 1939.
No Allied convoy was every destroyed in detail by U Boats
What does destroyed in detail mean? No 1940 Luftwaffe raid on Britain was destroyed in detail, so the RAF was never winning?
Thousands of merchant ships travelled alone outside convoys across the oceans from the start to the end of WWII
and were lost as a result.
The Germans were never winning.
The Germans/Axis were winning the tonnage war until around late 1942. On top of that comes the flow on effects, the bottleneck of merchant shipping then invasion shipping and their effects on allied operations. The high ship losses in 1942 caused the cancellation of many LST to be replaced by DE, more invasion shipping in 1944 would have enabled more allied operations, Overlord earlier plus Dragoon at the same time. The cost of allied ASW. Convoying cost cargo capacity, the wait times at either end increased, ships were idle for longer.
Figuring out how much shipping was lost in WWII runs into the lower tonnage limit used when compiling the figures otherwise think how many canoes make it as battle casualties, plus many histories only list the combat losses. In addition much officially neutral shipping was employed by the allies.
The book The Allied Convoy System by Arnold Hague seems to use 100 GRT as the lower limit, his figures are 6,428 ship losses, 2,775 to submarines, 753 to aircraft, 521 to mine, 326 to surface attack, other causes 411 (note the book says these include capture, being sunk by the explosion of another ship as the result of an attack, and unknown combat related causes), 307 foundered, 95 overdue presumed lost (some would be lost to submarine or surface raider), 226 fire and explosion, 312 collision and 702 wrecked. So the hazards of sailing in close proximity to other ships, without lights and lighthouses, sometimes more heavily loaded than normal, in weather that would usually be avoided in peace time meant that for every three losses related to enemy action there was one loss to marine causes.
The USN notes 302 marine losses in 1942, 620,266 GRT and 131 losses 278,269 GRT in the first 5 months of 1943, that loss rate over 5 years is about 3,000,000 GRT. The USSBS has the Japanese losing 116 ships, 308,386 GRT to marine causes.
Lloyds idea of losses, Total Shipping sunk by war related causes, are put at
1939 228 ships 781,747 GRT
1940 1,135 ships 3,993,198 GRT
1941 1,268 ships 3,964,111 GRT
1942 1,738 ships 7,645,339 GRT
1943 654 ships 3,235,378 GRT
1944 260 ships 1,175,797 GRT
1945 128 ships 519,078 GRT
Total 5,411 ships 21,314,648 GRT
Out of these neutral shipping sunk was,
1939 87 ships 252,135 GRT
1940 227 ships 678,368 GRT
1941 70 ships 214,248 GRT
1942 91 ships 267,988 GRT
1943 62 ships 82,137 GRT
1944 34 ships 26,051 GRT
1945 6 ships 1,505 GRT
Total 577 ships 1,522,432 GRT
Total captured ships (this is in addition to the sinkings above),
1939 15 ships 34,953 GRT
1940 205 ships 519,821 GRT
1941 375 ships 562,700 GRT
1942 133 ships 246,284 GRT
1943 9 ships 24,367 GRT
1944 13 ships 26,537 GRT
1945 3 ships 1,523 GRT
Total 753 ships 1,416,185 GRT
Out of which the neutral shipping captured was,
1939 13 ships 28,568 GRT
1940 63 ships 140,174 GRT
1941 13 ships 54,880 GRT
1942 1 ship 1,200 GRT
1943 1 ship 1,248 GRT
Total 91 ships 226,070 GRT
Lloyds list some 387 ships of 951,078 GRT as unknown reasons for loss. Cross referencing Axis Submarine Successes by Jurgen Rohwer accounts for half of these and most of the tonnage.
"British" tanker losses to end November 1941 were around 2.1 million tons, balanced by under 3.1 million tons of gains, mostly the tanker fleets of countries the Germans had invaded. (850,000 tons was new construction.). So the fleet was around 4.2 million tons then add the US fleet, though most of that was in US coastal trade. Allied tanker losses went to 1,859,000 DWT December 1941 to May 1942, another 754,000 DWT June to August 1942. The allied tanker fleet did not regain its November 1941 strength until around November 1943, the fleet spent most of 1942 to February 1943 down a nett 1.7 million GRT. That hurt allied operations. After 1943 the gains were more than a million tons per quarter more than the losses. Even so to help ease the shortage Independent voyages returning from Europe were used in 1944 and 1945.
Clay Blair has some of the best figures on Convoy losses, as opposed to independent sailings.
His figures for 1939 are 700 ships sailing from North America or Sierra Leone to Britain in convoy, 5 ships lost.
In 1940 5,434 ships sailing from North America or Sierra Leone to Britain in convoy, 133 ships lost.
In 1941 5,923 ships sailing from North America or Sierra Leone to Britain in convoy, 153 ships lost.
During this time period 19 convoys lost 6 or more ships, a total of 187 ships from the 19 convoys, worst hit was SC7 21 ships lost, in October 1940. So these 19 actions accounted for most of the 291 ships lost from convoys. Blair quotes US tenth fleet figures of North Atlantic convoys, 169 ships lost out of 7,558 in 1942, 139 out of 9,097 in 1943, 11 out of 12,907 in 1944 and 6 out of 5,857 in 1945. The carnage caused to HX229 and SC122 in March 1943 21 out of 94 ships sunk, 141,000 tons, made it look like the U-boats were able to break the convoy system.
According to the RN official history from January 1942 to May 1943 inclusive 537 ships were sunk in convoys (411 to subs), versus 1067 ships sailing independently (934 to subs). Even in the first 5 months of 1943 the convoys lost 193 ships versus 105 sailing independently. These figures are for all theatres of war and come after the requirements, like top speed, for sailing independently were increased in 1941. Going independent was dangerous.
The US merchant marine notes it sustained a higher casualty rate than any branch of the US Armed forces, Marine Corps included.
The Allied Convoy System by Hague notes total UK merchant sailor deaths for the war notified to the registrar general was 29,180, plus 814 lost on fishing vessels, these figures exclude British losses on other nationality's or requisitioned merchant ships and "foreign" (Lascar etc.) casualties on UK merchant ships.
The UK history Merchant Shipping And The Demands Of War comes up with an estimated figure of 43,886 deaths or "permanent damage" from all causes when estimating the total merchant sailors lost to the end of 1944, then comes the 1945 deaths, about 317 direct deaths plus those ashore etc. So maybe 45,000 deaths and permanent damage, of which at least 32,000 were deaths, compared with 60,595 dead and 86,162 seriously injured civilians in the UK from enemy attack.