There were a few Naomi upright drivers - Crazy Taxi, 18 Wheeler, Jumbo Safari - off the top of my head. They worked surprisingly well to be honest.
As far as lightgun go, I have played some Dreamcast lightgun games on one of my sit down Net Citys and it works great.

I tried to use the same set-up on a upright Naomi where the monitor is at the same height as that Confidential Mission cabinet (funnily enough it was a Confidential Mission cabinet that I converted to JAMMA) but the accuracy was terrible. I couldn't even get the guns to calibrate properly.
This is because the DC lightguns are meant to be used roughly at 90 degrees to the screen. When playing stood up at my sit down cab the barrel is at 90 degrees to the screen. When playing stood up at the stand up machine the barell is no longer at 90 and that's why it does not perform properly.
Confidential Mission and some other arcade shooters work using different technology (you can see the gun sensors in the bezel of that video) and so standing at an angle isn't an issue.
I have no experience with the aim tracks and don't know how they work but I would imagine they work on slanted screens as many peoples arcade cabs have slanted monitors. I'm sure someone will be able to tell you though.