I don't see an anti-shipping Me 163 as stupid at all especially if it was the longer ranged Me 263 version. The Me 263, BT 700 weapon and TSA-2D bombsight were all independantly developed weapons so the expense was only in integrating them. The range is given in "Luftwaffe Secret Projects: Ground attack and special purpose aircraft" as a radious of around 45 knautical miles or so (don't have book with me).
Once airborn they would be beyond interception. The weakiness is of course the range, it can protect only a narrow section of coast. These interceptors and their pilots would need to do double duty intercepting bombers or reconaisance aircraft using either these aircraft; otherwise they'd just be wasting time waiting for an invasion fleet on their stretch.
The strength of the weapon was its extremely potent weaponry the warhead is equal to a truely massive torpedo, its detonation in an area that can not be easily protecred, the expected high accuracy and pk and the difficulty in intercepting.
Ofcourse the Luftwaffe didn't atually decide to produce it; however they did investigate it.