The preferred drop altitute was 18,000 ft for the Fritz X, and lower than that for thev Hs 293, that's within the effective range of anything 5 in. and up. And within the possible range of smaller stuff.Hs.293 carried 12km of guidance wire specifically to keep the carrier aircraft outside effective AA range.
Enemy fighter aircraft are a different story. Carrier aircraft must have adequate fighter escort just like any other bomber.