i have problems with too many notifications that my server cant handle them.
in news when i want to send a news the page takes so much times to load.

of course i dont have this problem with cbb but maybe there is less notifications?
+22K registered users.

can i delete notifications from database with cron job?

I'm guessing you mean the PM's that the notifications cause to clutter the dB? If so try MP Manager HERE

Or perhaps you actually want to remove the notifications... if so the best thing would be to disable them in the admin section of the module(s) causing issues (news). Trying to remove them for 20k users from the dB seems just silly when you can just turn notifications off per module... If you want to, you could try limiting the notification options and see if that helps as well.