Repair of specialized equipment is a big deal, too. In many cases it takes as much skill as fabricating an apparatus in the first place.
Like the article says, it helps a lot if the glassblower understands the scientific process and works closely with the researcher. I think researchers work around this by finding ways to use or combine standard equipment. A scientist doing truly novel work, though, will benefit from or require customized glassware.
My belief is that this will be solved by 3-D printing or automation in some way.