Microswitches rarely suddenly 100% stop working. Through contact wear they usually start out becoming intermittent, common failure mode is they make contact only at the moment of switch but then lose contact when held down and it eventually gets worse.

I've never owned a Nine Ball so can't say but it seems there are potentially software issues at play here.
Testing the micro-switch a number of times with your multi-meter will usually tell you if they're suspect. Personally I find analog meters are better for this because quick dropouts are more noticeable with analog needle deflection.

Judging by the hand written labels on U1 and U5, any chance you can dump them and check them against the Nine Ball ROMs on IPDB? maybe you have an alternate factory version??

Not sure if you also noticed the playfield picture of that machine had green 1 & 9 balls in the bonus area instead of yellow and the left side drop targets are blue though they likely aren't original.

Nineball_Playfield2.jpg

See here:
https://pinside.com/pinball/forum/topic/price-check-1980-sterns-quicksilver-stargazer-seawitch/page/158#post-7407859

Actually I'll add the Nine Ball lamp driver board repro here too:

Lightning_to_Nineball_LampDriverBoard_GameOver-Tilt_WireColor_Fixed.pdf

Well, all the other Stern schematics I looked at match your games wire colors. So I'd say the Nine Ball playfield schematic is wrong (no surprise).
I've updated the lamp driver board schematic in my previous post.

Not unusual. Bally and Stern did a lot of it. I was working on a Bally Viking not long ago and three solenoids have a Black-Red wire. Ran back to different connectors but not like there were so many coils they were running out of wire color options.