It's almost always a non-issue.
Keep in mind that keyboards and pitched percussion are really the extent of the fixed-frequency instruments. All wind instruments use the breath, embouchure, and occasionally tuning slide adjustments or alternate fingerings to adjust tuning on the small scale.
Even guitarists have some options for tuning adjustment, but their instrument has so many other tuning idiosyncrasies to take into account that I'm sure just intonation gets a serious back seat.
Similarly, in the situations I'll bet you're thinking about (like a guitar or piano concerto), the piece of music is going to be so melodically active that it's highly unlikely the audience will notice: the orchestra or ensemble might play a sustained chord (that they can adjust as necessary) and the soloist will be playing lots and lots of notes over this chord, not one of them held long enough to notice if it's not perfectly in-tune with the rest of the group. Also, the audience ear is used to hearing the piano with its equally-tempered tuning system (not to mention how by the end of a Liszt concerto the strings may have gone slightly out of tune from the performance itself).
Instruments like pipe organ and many pitched percussion have timbral qualities that cause them to take up a huge area of the harmonic spectrum on even a single note, further masking tuning issues and instead recasting them to the ear as brightness of tone.
I've left out vocalists up to this point, and not unintentionally... singers, in general, and somewhat ironically, typically just don't have as good ears as instrumentalists. Any conservatory theory/aural skills professor, at least in the US, will hold this to be true. You will be hard pressed to find even professional choirs that sing well enough in-tune for this to be an issue, and that kind of ensemble is either going to be singing a cappella or with orchestral (or perhaps organ) accompaniment. Piano as choral accompaniment is really common in school and church choirs (admittedly, the majority) where the level of performance is below the threshold of this being an issue. There are exceptions, of course (some newer pieces by Eric Whitacre come to mind), but that usually falls into the category of highly active melody/harmony or familiarity with piano intonation (the piano is the quintessential choral rehearsal instrument, after all).