Yes.
If the headphone/earbud/IEM you're equalizing is sensitive and you overdrive them at some frequency, you can blow out the driver or break it's suspension, yes. For instance if you tried to up the bass on headphones that don't have too much of it anyway, and didn't get more bass as you wished but kept raising the equalizer up, it will eventually break out of physical strain, or burn out the coils. Foobar2000 goes up to +20dB, that is easily enough to break a headphone if the volume accidentally goes way too high.
A distorting amplifier can break tweeters, I'm sure distorting amplifiers can blow a headphone driver too if you try some ludicrous equalizing.
Better be careful and always equalize with your headphones on at comfortable listening levels.