Gonna answer these question is order as they appear in your post
It's really up to personal prefernece. I prefer to have physical copies cause I have multiple systems. But there's nothing wrong with having a digital copy.
I don't think Nintendo sells the NL copy, they only seem to sell the NLWA copy. If you buy a copy labeld as WA, then you dont need to download the update, it's already in the game. I have 2 copies like that. Downloading will not mess up any data.
Yes it should connect online, just as the first copy does.
Because I have only physical copies here's what I know:
Let's say you tag someone not you. Cool. The way it works is that if you had town A in the system but don't play town A and instead put in/turned on town B, town B will get that streetpass and town A won't. However, if you get tagged, play with town A, that tag goes to town A, not B. I assume the same would apply for a digital copy.
You may have to relink HHD to the second town. I don't have HHD, so I can't say for sure.
There should be no reasonable way that the 2 towns would interact or corrupt in anyway on the same system.
If you want more explanation feel free to ask!