In general, you are right. Scolipede is a lot bulkier than Ninjask so might be preferable as a Baton Passer. It also isn't 4x weak to Stealth Rocks, which is definitely a bonus.
The only situation I can think of (aside from the Sticky Web you mentioned) where Ninjask might be preferable is if it is necessary for you to move first on the first turn. Scolipede is pretty fast, but Ninjask is the second fastest Pokemon in the game (just slightly behind Deoxys-S), so will move before all non-scarfed opponents (priority excluded, of course). Of course, Scolipede can just Protect on the first turn if it wants to make sure it is faster, so even this isn't a particularly great advantage.
So, in short, I think Ninjask is pretty much outclassed now.
To add insult to injury, Scolipede also gets access to some entry hazards (it can get both Spikes and Toxic Spikes), making it a potential all-round utility Pokemon. It also gets a powerful STAB move, Mega Horn, which is something else that Ninjask lacks, although since it is a Baton Passer it doesn't really need it, but still it is something else to note.