I remember doing this in the past and madVR was ok but I had issues when other programs tried to use LAV Filters. Is this recommended now?
I don't know about recommended, but I've had no issues with it and have been doing that for years.
What is the harm in running different installs of madVR - latest that works with MC, latest that works with Zoom Player, latest that works with MPC-BE, etc... As long as they are put into the correct directories?
There's no harm in it, but now you're managing multiple (potentially) different versions of madVR and settings for each.
That's far too much hassle for me.
I keep one install of madVR (in the MC plugins directory) and use profile groups if I want different settings for other media players.
For example:
if (mediaPlayer = "mpc-be64.exe") "mpc-be"
else "default"
I use this rule for a profile group so that MPC-BE has all post-processing disabled and the queue sizes set to the minimum, as I typically only use it for things like scanning through files to look for a specific timecode or taking screenshots and want it to be as responsive as possible.