Certainly.
If you get paid, and you're consistently late, for no good reason, your pay should be docked.
The original question included, should they be docked for not playing for Sunday School, evening Services, etc etc. That all depends on the agreement between the church and musician. If you don't get extra money to play for those things, and don't show up, then no, you shouldn't be docked at all, if its not included your overall total pay.