Time... RTC modules are pretty cheap if you shop. In fact, if you do a deal with Yourduino (Terry King) for the DS18B20's, see about Real Time Clock modules as well. Bigger deal should get bigger discount?
Worst thing I find about Yourduino is that the prices are so low the shipping ends up a larger part of the total, but I guess he could raise prices so that wouldn't be true.
If you run cables then you should be able to use them to power the data collectors. You could also run time signal through the cables.
How many hives will you be getting data from at once? Each will give how many bytes of data per hour? And I feel sure that you will need at least 12V for long cable data transmission, but my experience on that is old and that may no longer be true.
Can you get the temperature of the air the bees circulate, even just at the exits?
Can you put pyrometers above the space between the frames? You might not have to do them all if you can extrapolate from the ones that have both.