Can someone explain why this happens?
On block it pulls them in, on hit it pushes them away, with Lenny the super's hitstop allows the item to combo off the launcher because it only affects the opponent, thus you get the on-hit reaction.
Not sure which bit you're asking about, but that's all of them. :^P Nothing particularly odd.
(In case you are curious, they pull in on block because they are a very strong zoning tool that is hard to avoid, so having the pull in on block makes it slightly weaker. They pull in on OTG because of a bug, but I left it because it's cool.)
I feel like I should really know whether or not it [hitstop] usually affects projectiles.
Hitstop from hits in most well-made fighting game only affects the two objects involved in the hit.
Superflash hitstop only affects the opponent (not projectiles) in ST, COTA-MSH-XSF up to MvC2, the SFA series, 3s, etc. You can, for example, do a fullscreen Sentinel cr.Fierce xx HSF which will not combo, but if you DHC the HSF to any other super, the DHC adds like 2-3f more hitstop and the drones will combo off the cr.Fierce.
Superflash pause does not affect certain projectiles in Guilty Gear, like May's dolphin hoop.
You can also use this to set up post-flash unblockables in all the listed Capcom games by having a projectile that makes contact with the opponent during the hitstop period - if they were not blocking preflash they can't block. The does not work in GG.
Interestingly, hitstop from projectile impacts affects EVERYTHING in Killer Instinct 1, which makes the game feel really damn weird. And in some cases it affects everything in KI3, too.