Large sites

Having the players conquer large sites can be rewarding. And it certainly looks cool to have a large site many nodes and connections.

Large sites are nice in that they give you the opportunity to do environmental storytelling with the names of the nodes and layers that don't do anything (when hacked) but do indicate what the site is for.

They are also very good for having the players explore. You can build puzzles around having to scout around the site to find a password, without actually having to hack ICE to progress.

Site reset for larger sites

If the site is large, having the entire site reset can be annoying. It's not fun for players to hack a lot of ICE just to get to the same point. One options is to split a larger site into different sections. Each section has tripwires, some ICE to overcome, and the payout. Near the payout is also a core layer that allows resetting the tripwire. That way, players can overcome the site a section at a time. If they fail to hack a section, they still have the progress of the previous sections, so only need to re-hack the last section.