That seems improbable. Bulletproof glass is several cm thick, which would make the array prohibitively heavy. Some solar arrays are so thin they can be rolled up. I'd expect there to be no cover at all.
Very interesting. Is there any pics of the punctured solar arrays?
The solar arrays on the ISS also have several small holes in them.
MMOD damage is something that solar panel designers have to keep in mind for space-based applications - mainly by including redundant wiring so damage to a solar cell does not take out the entire array. There's not much else you can do about it.
Also, bullets travel much, much slower than objects in orbit do. Orbital velocity at the altitude of the ISS is about 7.8 km/s. High velocity rifle rounds can be around 1.2 km/s. Subsonic rounds go 400 m/s. Bulletproof glass just isn't designed to handle the energy of objects going at orbital velocity.