Why not just try it. You might lose some modules you don't have access to in the base game, but if that's all you can run it doesn't matter does it?
I've sometimes wondered about basic stuff like what'd happen if I was flying, say, a Beluga or Dolphin and then swapped from Horizons to Vanilla, but it's never bothered me enough to actually test it out.
I'm guessing that FDev have set the Vanilla game up so it's compatible with all the Horizons assets (ships, engineering etc) so that a Horizons player doesn't lose anything when they swap to Vanilla whereas a Vanilla-only player simply won't ever have had the opportunity to obtain any Horizons assets so they're never going to see them.
FDev don't always get things right but the way they've handled backward-compatibility between Horizons and Vanilla seems to be faultless.
About the closest I've seen to a "problem" is when they've initiated stuff like CGs that are open to everybody but which only Horizons owners can participate in because they've required players to visit Horizons-only locations.
I don't really see that as a "fault", though, any more than if they announced, for example, a mining CG which I could sign-up for but then couldn't participate in because I didn't have a mining ship.