Consider bits 5...6 have been introduced to actually report the type of water more consistently than before, including whether there is water at all.
IMO, this is something like a "hack". In fact, it seems that unfortunately nobody ever noticed the lack of such a check (i.e., outside a CB). But to have more than one var for the same thing, with both reporting different facts is something which needs getting used to, to say the least.
Changing the meaning and behaviour of the other bits, especially bit 1, as you suggested would have broken (some) existing (industry) NewGRFs.
I don´t think so. Both of my proposals would be downward compatible. W/r to var41 (I would have prefered that solution), bit 4 hasn´t been in use at all, and w/r to var60/62 bit1, there´s no real use for it in this context, except checking it when in a CB (i.e. before object/industry tile is actually being built), so no problem with older sets.
Anyway, thanks for your response.