It gets easier to tell the more you listen to different bards, but the main difference is usually in the rhythm; manual bards have to deal with input lag while they hear themselves play, so you might notice small changes in timing as the song progresses. They’re also more likely to make human mistakes like playing a wrong note here or there, whereas MIDI software will typically play without errors from start to finish. (MIDIs are not perfect though, a MIDI player could occasionally make more extreme errors like abruptly ending the song early, or skipping an entire section of a song due to lag)

You might also notice instrumental differences as well, most manual bards seem to favor instruments without chords, as it is especially difficult (but not impossible) to play chords manually in FFXIV. There are workarounds to this, such as using third party software to connect a real piano keyboard, but the way to do it without any mods at all is to arpeggiate your chords. (to slightly space out the timing in between each note of the chord, played like an arpeggio)

Another way to tell could just be the number of bards; manual bards are almost exclusively solo players, though there are rare exceptions. Chances are if you see two or more bards playing together, they are probably using MIDI software. FFXIV does include an ensemble feature to help bands play and keep time using a metronome, it’s just not used often as it takes considerable skill and coordination between everyone involved.

Also most bards are pretty open about what method they are using, so if you’re ever not sure you can always just ask. (I mostly just play MIDIs I’ve edited myself, so unless a video I post has [Manual] in the title, then it would be a MIDI)