To be more specific, the windows which hold the water in the secret area.

What exactly is the proper ZDoom solution for this? The windows use 3DMidTex, but that doesn't seem to stop hitscans and there isn't any combination of flags I know of that will make this work.

You could use a thin, solid, translucent 3d floor instead?

That's like killing a fly with a sledgehammer, though.

It will work, but I avoided doing so in case there's a better UDMF-y way that someone knows about.

This is still an issue, so I'd assume there isn't a better way that somebody knows about!

I'd otherwise suggest a good ol' vanilla HOM trick - raising a thin sector's floor 1px below the ceiling - but considering you could go over that line, you could notice the HOM. Not sure how else to fix this other than with a 3d floor...

I've replaced the windows with a translucent 3D floor. Can't think of anything else that won't cause some other issue.