Could've been any number of relatively minor things... An AA going out of commission and needing repair, problem with some of the show sounds, etc. Heck, first time I rode DL's PotC, they shut down the ride behind us because all of the show lighting went out in the last three scenes.
Rides randomly go down for parts of the day all the time. Stuff happens :shrug: If it's not a major problem, they'll usually fix it and re-open it before the day is out.
Was Jungle Cruise down at any point too? Typically when they shut down Pirates, they also shut down Jungle Cruise, as the extra cast members they have at Jungle Cruise are used to help evac Pirates.
I was there on the 3rd and though I didn't ride it, I noticed there were lines as if it were up and running. Maybe they closed it down AFTER I left? Hmm. I do know that when I rode it the day after that it looked like it was having trouble - the part where you pass through the mist/Davey Jones wasn't working. No mist, no squidface...only his voice. It was working normally by the 2nd time I rode it that day.