A lot of that went over my head for right now, lol, but I'll reference it again before I kick the server off. I think you did just confirm it's going to be the pain in the butt I thought it was going to be, though.
If you're running one of the premade (FTB or otherwise) packs, you can simply backup everything (always backup regularly anyway, but especially before updates) then update your client with little issue. Most of the pain in the butt has been done already, in that the mods have all been tested for stability and compatibility before FTB will push the update. Once you're sure your client works to your satisfaction, you can simply copy the mods folder over (disregarding any client side mods) and test the server. If it boots, log in and do a walkthrough. If issues arise, roll back to the backups. If not, let your players know what version the server is running, and everything should be fine.
If you are maintaining your own pack,
@Henry Link takes a fair approach. Maintaining your own pack is always more pain because all the testing is done on your end by you. In this case, updating small groups of mods at once is recommended, else trying to nail down any potential conflicts is more difficult.
Usually, I don't bother updating mods unless they have fixed something that could corrupt my world, fixed a bug I'm currently encountering, or added new content that I want to play with. That said, any pack I put together is for myself and a few friends at most, so I don't feel the responsibility that comes with maintaining a public pack.