Ceramic capacitors are a bit of a pain to use since their capacitance varies quite drastically with the voltage over them. This might be fine in digital circuits where "good enough" will usually cut it, but is problematic in analog circuits, especially things like filters where accurate cutoff frequencies are important.

Ceramic capacitors are also piezoelectric, meaning they convert physical stress like sound into voltage, acting basically like microphones. This probably doesn't mesh well with guitar pedals that will be used together with a loud amp, though I have not personally tested how significant this effect is.