Yes, it is, but they aren't turned on by default, because there is a slight complication: The maps that come with Quake don't have vis'ed water, which means if you make the water transparent, you will encounter graphics bugs. During the compilation of the maps to the format of the game, some data (which visleaf is visible from other visleafes) is calculated to speed up the rendering. Because the waters is assumend to be opaque, the game doesn't render the other side.
The variable r_wateralpha determins, how translucent the water is. 1 is opaque and 0 is completely invisble. It's only possible to change it for all liquids at the same time.
You have to used map files with updated visibility data, otherwise you will get ugly graphical glitches. There is a program called vispatch to update the vanilla maps.
Hmm, I can't remember ever vispatching id1, hipnotic and rogue, but I must have done as they work fine in DarkPlaces with the water surface transparency. Well, time to go looking for vispatch data for Abyss of Pandemonium then.
I would imagine that vispatched maps don't cause an issue with ports that don't use water surface transparency, as they would just result in redundant data due to the water surface not showing what was underneath anyway. I'll have to have a play around and see.
Quakespam doesn't work for me. I get the exact same error message (except with the Quakespam.exe).
In that case I don't think it is the game causing the issue, but your Operating System.
I Googled the error message and found this: http://answers.microsoft.com/en-us/windows/forum/windows_7-windows_programs/error-0xc0000005-when-ever-i-try-to-do-anything/568af1bf-b998-47af-a9cf-9373ae735100?page=1
That points at Windows Updates KB2872339 and KB2882822 being the cause of Error 0xc0000005.
It lists the fix as uninstalling these updates. You can do this via Windows Update or by running a command in the command prompt. For example: wusa.exe /uninstall /kb:2872339
Good luck with this.