Hello!
Yes, most glitches are allowed on our server. There is a commen glitch allowing players to get past 1 set of doors. I reccomend not having doors in your base and just using /sethome and then using /home to return to your base. That should prevent people from glitching in. Also, it is possible someone used the vclip hack to get into your base. In case you don't know, vclip is a hack allowing someone to teleport down, usually to get into your base. If you see someone on your roof, start recording (if you can) to get evidence of them vclipping and then report it here.
I hope this helped,
-Panda