The RN would have commited its older World War one vessels to the invasion area. The old girls would have taken high casualties but they were expected to the Royal Navy has never shied away from high casualties. The thought of flotillas of destroyers and light cruisers running amok amongst the unseaworthy river barges night after night would give the German Army and the Navy ulcers and white hair. No matter what the Germans do the Channel belongs to the RN at night.
With only about 13 hours of daylight the Germans are never going to have a hope of supplying the troops they can land. A Rhine river barge is a slow old beast the barges of the time would probably do at best 6 knots and in the channel 6 knot currents are the norm so sailing times are going to be limited. In an ideal world a barge could make the trip to the invasion beach during the day unload overnight on the beach if the tides are right make the trip back home the next day. Reload overnight and be ready to make the trip back again. This is in an ideal world which never ever happens in logistics even today with computers running things. The ports in France Belgium and Holland are going to be chaos loading even a barge needs cranes quays and lots and lots of men. The Germans have to get the cargoes to the right ports and then in the right barges you cant just throw everything in willy nilly, sailing orders need to be written, escorts need to be available. All this while the RAF and the RN is sticking its nose in. Then there is the problem of a shrinking pool of barges. Casualties especially to the unpowered barges that were to be towed by tugs would be frightening. The thought of trying to tow a string of barges in the channel makes me go a bit queasy just thinking about it. I think 5% casualties per trip for the barges would not be excessive anyone can do the maths.
A lot of Sealion enthusiasts get hung up on the weapons and tactics but completely forget the logistics. The troops that landed would be eating there boots and drinking out of puddles within days. I dont know how much stores a division needs per day but a fighting man needs at least 3,000 calories and 2 litres of water per day to keep on fighting. I imagine the best and simplest way to defeat the invasion is to concentrate on holding the Germans in the landing area and waiting till they run out of food or ammunition then escorting the survivors to the POW camps. The Allies in June 44 had near Jesus walking on water levels of shipping and even then supplies were sometimes a bit short till they captured a port and got it working.
The only way I can see a succesful Sealionn is for the Germans to build thousands of proper landing craft, hundreds of heavy lift ships with cranes and derricks to offload at sea and thousands of short field transport aircraft. All of those things take time, design effort, building capacity and money. Then the Germans need at least a year of training, at least one major practice invasion to get all the bugs out of the system and they have to do all this without British intelligence noticing.
Meanwhile nice old Uncle Joe in the east is rebuilding his army and building lots and lots and lots of T34 tanks. What could possibly go wrong for the Germans.