I'm reasonably sure the lag would continue if you weren't using ULX and just plain Gmod/Source ban system to begin with.
How large is your gmod/cfg/banned_users.cfg ?
I'd say it's quite large too, and it only stores steam_id.
You could potentially remove/delete the data/ulib/bans.txt, but you then lose reason/name of banned/name of banner and any temporary bans.
We're looking towards sqllite and sql capability in the future, but, it's going to be some time, and even so, sqlite may not be a huge improvement for a ban file that large.