Generally, you can delete all but the most recent versions of all mods except for MediaVPs and probably FSPort/FSPort-MediaVPs. These are the "base" mods that are used as a requirement by the majority of existing mods, and many of these mods can rely on older versions of these.
I personally force whatever mods I play to use the latest and greatest MediaVPs by making a brute force modification in their mod.json file - replacing MediaVPs dependency version with 4.3.3 (at the moment). This is NOT supported, and quite likely to cause issues in case of more advanced mods, so your mileage may vary wildly. Although I'd personally say that most retail-like mods (Homesick, Sync, Uncharted Territory...) are pretty safe to have this done to them, lately I also forced The Aftermath: Reboot in the same way and found no real issues across the bunch of missions I tried.
Also, Blue Planet *does* have some mods that use it as a dependency. I recall that Mantle and Friends and Foes relied on some quite old version of BP, and there's Blue Planet: Battle Captains and possibly VOTC that might do so also. I think the rest of BP-reliant mods (Battle of Neptune, Warmachine, incoming Mote in the Sunbeam) should be happy with the most recent version.
