Question on stacking

[The KrijnMinister]

There are optional rules that do exactly what you are saying; inflict more casualties the more populated a hex. I believe they are the alternate fire resolution rules.

Regarding your crossing the river question; it depends what is more important to you:
If your unit cannot get out of T-mode after crossing, then yes it is prone to suffering more casualties next turn.
You will have to weigh what is more important; preserving your local force numbers, or getting more assets across the river asap.

I would have usually always preferred not incurring the inflated losses, but my current opponent in a Minsk campaign game is using Engineer river ferrying on a massive scale, presenting me with more T-mode units than I can hit. It has been very effective and an eye opener