1) I am one of the the programmer/developers, so yep, I might just know a thing or two
2) Mines can go in shallow water, maybe dragons teeth as well IIRC, but definately no defences in deep water. (Forget if shallow is only-1, may be -2 level, I dont design scenarios and havent played a beach assault in yonks)
3) landing craft (with radios?) that are 0 units (IIRC)
do have the ability to spot. Otherwise, you cannot adjust or call for fire as you boat into land.
That was, again IIRC, one of the problems in the original DOS game that I changed the code for. (If you had say some helos (MBT, late WW2) or I think, warships, they could spot and call for fires in the original SSI DOS games - trying to think back 20+ years there!).
4) Trenches are a bit odd at times. The are part terrain tile and part defence obstacle (they can remove trees etc IIRC in the hex they are plotted into). Stick with using them away from water I would say, they can be useful as anti tank ditches (if you play with breakdowns on)
5) Water has always been a bugbear of the game from the start as to weird things that can happen. We have caught some and likely added new weirds as the years went by. It is the AI that has problems on maps with deeper warter, especially if it is not a properly designed river crossing or beach assault scenario, and especially with regards to path finding navigation.
Little offshore sandbanks may not confuse a human player of a beach assault scenario, but the AI will happly unload onto them, perhaps leaving some units twiddling their thumbs there...
A river crossing that has two rivers might look dead cool to the designer, and a human probably can handle that if he can get his barges alive to the second one, The AI wont as its stock behaviour is soley based on there being
precisely one water obstacle - it will happily ferry units to the far bank of river #1, but simply wont have a clue what to do about river #2 (or some inland lake you added "just because" sitting behind river #1)...