We can only use them in Cyrodiil.
I made my brother play the IC main quest recently and I had forgotten that they use Ballistae in the final mission to fend off a hoard of enemies.
It's the ONLY time I've ever seen siege weapons being used in story content.

Then we recently ventured into the deadlands and saw this massive four-armed dude walking towards us.
I know they're just there for decoration, but how cool would've been if we could spawn siege weapons and start blasting him from a distance before he got near and crushed us?
Something simple as that could completely spice up stories to make gameplay more engaging.
Heck, even the final boss in Blackwood has a cool monster in the background I think would be nice to shoot at with a catapult to keep at bay while you fight the small boss in front of you (I'm just trying to avoid spoilers but I'm sure everyone knows what I'm talking about at this point).
Even public events like those would be nice, Siege weapons are accessible to everyone without needing DLC's, they can be purchased with AP or Gold, so it's not like it would force players into PvP, and the idea that imperial city was PvPvE had me excited to think that we could use siege weapons against gigantic monsters in imperial city (which sadly wasn't the case)

Maybe with the expansion we get to see ships approaching so we can use siege weapons to try to destroy them before they reach the main land?
I dunno, I just think there's a lot of potential to use them other than just Cyrodiil's sieges.
I don't think anybody cares that they can't destroy PvE buildings anyway, and they've been nerfed against NPC's too, so I doubt they could be use to maximize DPS (considering important bosses are in-doors and wouldn't have room to actually use a siege weapon other than ballistae and dwemer gatling guns, forgot their names).