The glass ball is part of the "housing pressure regulator." It keeps internal housing pressure at around 4 PSI. Running without it lowers the internal pressure to zero which in itself, hurts nothing. Plugging is an indicator of other problems - as you already know.
When the ball is plugged, housing pressure gets so high - it exceeds feed-fuel charge pressure and essentially shuts the pump down.
Probably all you need is $25 in parts to fix back to original, or for an extra $50 - you can eliminate that pellathane/plastic dampener ring.
By the way, that housing regulator valve also serves as an anti-drain back fuel check valve. When removed it can cause some equipment to get air in the fuel after sitting. Mostly a problem with cars and pickup trucks that have fuel tanks mounted far away from the pump and often sitting lower then the pump. Chevy had many cold-start problems in 6.2 and a few 6.5 diesels when that ball-valve leaked or got stuck.