I do think those cards tend to be unpopular. Well they are unpopular among the group that talks loudly online. We always enjoy it when there's e.g. Sacred Grove in a game and it means that you'll be randomly getting some Boons from other players. But some people are all "I'd be such a fool if I helped them win" and shun that family of cards. The cards end up looking bad when they're fair.
I do them anyway in small quantities because they provide non-attack player interaction and well surely someone else likes them.
I don't think that's quite true. Governor is a clear counter-example. Top players and the forum crowd love Governor, and the friendly interaction is what makes it so interesting and difficult. It's also very strong, but then Bishop is a good example of a friendly interactive card that's generally liked despite being mid-strength. Bishop is very interesting because it's occasionally a powerhouse and the crux of a good strategy, but often it's not as powerful as it looks, and you need to be very careful about the friendly interaction.
Generally, I don't think there's a dislike for friendly interactive cards among the top players and forum posters. Yes, they're not all filling the top of the Qvist rankings, but those are power rankings, not rankings of how much we appreciate the cards as interesting and fun additions to dominion. Yes, very weak cards tend to be disliked, but so do overpowered ones. As well as Governor and Bishop, Lost City is a friendly interactive card that is very appreciated by skilled players, and the interaction is, once again, a huge part of that. Deciding at what points in the game the interaction is most helpful to your opponents and therefore what points are bad times to buy lost city is difficult and interesting. Council Room is generally considered weak, yes, but it's not disliked. Nobody raves about Duchess, but again that's nothing to do with the friendly interaction, it's just a fairly weak card in most situations. Vault and Embassy are friendly interactive cards that used to be a bit panned by some sections of the community, but that's because they were viewed as overpowered BM enablers just like JoaT was. The dislike was unrelated to the friendly interaction. And those dislikes have mostly gone away as BM has become less relevant. Messenger isn't a favourite but I've not seen anyone point out the friendly interaction as a problem. Often it's quite cool. Yes, Sacred Grove isn't liked by high-level players, but that's not really because it has a friendly interaction, it's because that friendly interaction is unpredictable and swingy. People dislike Swindler for similar reasons.
I guess I'm saying, next time you're designing a set, I'd be sad to think that you were considering friendly interactions only as something for the casual players and that won't be appreciated by the hardcore, just because Sacred Grove hasn't gone down a storm with the latter group. My observations of forum posting (which lines up with my own opinions on the cards) is that top level players actually quite like friendly interactions and see them as interesting and challenging, they just don't like it when that friendly interaction is unpredictable and swingy, which the boons when received off-turn certainly are, more than hexes off-turn and boons on-turn (the normal way round to get them), and probably more so than hexes on-turn (from Cursed Village, which is also a friendly interaction I suppose - hexing yourself is helping your opponents (though this could open up a huge can of worms as to what a friendly interaction actually is so don't hold me to this semantic judgement) - and Cursed Village is another generally liked card.)