For me, it's only an issue if I don't really enjoy the LIs, which is its own problem. For example, I really like Hidaka and Chihiro from UN:LOGICAL, but since I also really like the designs of all of the LIs, the MC, and other characters that I don't have the "ack I wish you were an LI" urge with, it becomes "wow I love the character design of this game!" rather than a nagging issue. Comparatively, I like virtually every side character's design in Neon Clash better than how the LIs are designed (no offense intended to anyone who does like them, they're just not my style), so it basically killed my interest in the game www.
I don't have any personal experience reading a fandisc that adds a route for a side character, but hypothetically I think it depends on a lot of factors like the amount of time between the original game and the fandisc, (eg, if it's quick, then the likelihood that they purposefully are utilizing the character as a pull factor for sales is pretty high, which sucks) the quality of the route, how cohesive it is with the rest of the story (though, ironically, if it's too cohesive, it may have the reverse-effect of "why wasn't this in the original game in the first place?!" which will just annoy me more...) It's a pretty finicky concept for me. I mean ultimately, I understand needing to sell your game so... lol. If I like the character, it's still bittersweet and if I don't really care it's kind of lame... what a lose-lose situation for my brain.
I feel like I'm rambling at this point so I'll cut myself off. Ultimately, I prefer to view this as a problem of how compelling the LIs are rather than liking a side character being an issue. In fact, most of the side characters I pine for utilize their side-character status to the fullest and wouldn't really fit as LIs in the first place (thinking specifically of YUE from Blackish House here). Maybe the way to fix this feeling is to get really nerdy about narrative structure... I'm rambling again...