This was confirmed by Mark Keiser (Retlaw 72-76 Security 77-81) Summer
1974 "The guy that shot there presumably also shot the hole in the last
or second to last window of the Primeval World diorama. Later
investigation determined the hole to be .22 caliber (in both places), and
bullet fragments matched (courtesy of Anaheim PD) the holes in Adventures
in Inner Space (he shot up the snow flakes)."
There is another bullet sized hole beneath the duelist on the right, so
perhaps a deranged guest was shooting at "the man with the gun".
They knew that to replace the glass they'd have to take the roof off the
building first, so they decided to simply disguise it as a spider web.
BTW, there is a spare pane in the back lot.
A bit of trivia: the organ being played by the mad organist in the
ballroom is the actual movie prop organ from 20000 Leagues Under the Sea.