I just read about Maya time and the Long Count, too, and noticed the same thing. I read they could pinpoint eclipses and that their Venus cycle erred by only two hours for periods covering 500 years. That to me implies they had a finer unit of time than the day…but then their calender was 365 days long and perhaps if they were keeping track of time with a finer unit, they would have known that 365 was a little shy of the actual cycle.
This site says the smallest unit of the Long Count was indeed the day. If they figured out there were roughly 365 days in the solar calendar, though, it would not have been much of a challenge to devise hours, minutes, or seconds. What a great question!
I don’t think the Wikipedia article you linked mentions the Great Cycle: 20 tuns = 1 katun; 20 katun = 1 baktun; 13 baktuns = 1 Great Cycle.. The first Great Cycle started on 8/11/3114 BC and ends on 12/23/2012 AD, which is why 2012 is significant. Src: Guate Lonely Planet guidebook.