I was wondering if there was a way to make the motd not pop up on entering a server.
If you're a host of the server you're speaking of, yes.
The file to edit is mentioned in the addons/ulx_readme.txt ... server.ini
Many settings are set there, including the motd.
If you make any changes to your server.ini , make sure to Save As ... gmod/cfg , not back in addons/ulx/cfg, as that will get overwritten next update (Release or SVN)
If you aren't the server host, then no. ULX Motd is controlled by the server.