Vanguard units with jump packs can deepstrike and assault when they come in (Heroic Intervention special rule),
As long as they have no characters attached.
Right. So, bottom line, if you're deep striking, you're not charging (save for those very rare exceptions - and like CoD said, even they have caveats).
Do people use special weapon squads in IG armies at all? Or are they too fragile?
I have way too many special weapons to actually use them all otherwise.
Al'rahem's platoon:
-Command Squad with Al, 4 Plasma guns, Chimera
-2 Infantry squads with lasguns and flamers
-2 Special Weapon squads with meltaguns
I run an all reserves list with an Astropath. Only thing coming on my table edge is Straken, Nork and command squad, plus a veteran squad of shotguns and meltaguns - both in Chimeras. The platoon is designed to swarm infantry while dropping a vehicle or two sitting in the back (lots of plasma, lots of melta, plus the multi-laser on flanks/rear armor). Throw in "She's Like the Wind" (and the obligatory tune to carry the order), and you got some shooty + moving into cover afterward, oftentimes to take the objective or consolidate gained ground. Depending on rolls, Valkyries with Penal Legions and/or autocannon/HK missile Sentinels (who replaced my poor Kroot...) are there to provide additional support.
So yes, special weapon squads are good, unless you're ridin' dirty in Chimeras all across the battlefield (in which case you use Vets). My list uses them in a different roll and as part of a large ambush setup.
Another question: do you have to roll to hit with the primaris psyker's lightning arc power? Using his BS of 3 or 4 or whatever it is? If so it's not as good as I thought.
Yes. It isn't like WHFB where you have different classes of psychic powers. If it shoots, it's basically just their "weapon", albeit a bit stronger (most of the time).