What does this mean if I have an upgrade on the HQ? Can I tell the runner to access just 1 or 2 cards from my hand and he does not get to access that upgrade? Would seem kind of OP this way.
So if they have Legwork - then I have to pick 3 cards and they pick in which order they access those? Or do I give 1, then another 1 and so on?
DNN says you choose which cards the runner accesses from HQ, not in the root of HQ. The runner always accesses all cards in the root of a central server, and can intersperse those accesses with the access(es) they are making from cards in the server. Look at the official FAQ under multiple accesses.
Accessing an upgrade in the root of HQ is not optional, so you couldn’t choose that. Presumably the Runner gets to still choose access order (as there’s nothing to say that changes). Things in the root of HQ are not “in HQ” anyway, it’s a subtle distinction for central servers.
Easy to confuse, as upgrades in a remote are considered to be in that remote. But yeah, as already mentioned, DNN doesn’t affect upgrades in any meaningful way.
A scored DNN and Prisec/Product Placements are turning out to be really solid HQ defense out of Nisei Division. I’m quite liking it.
off topic, but are you speaking from experience? just curious, haven’t seen any Nesei decks around lately. 
I haven’t played on Jnet for a few weeks but last time I was rocking a Nisei deck, yeah. They are in a pretty good place right now.