Oh, emeralds are nigh impossible to obtain, guess I'll work towards emerald bees.
I found the gemmed bees to be a bit of a trap, as (at least under MindCrack?) you only get dust out of them.
Say for example you get yourself a diamond bee. Four full dust piles, placed into the implosion compressor, nets you three (industrial) diamonds. But for the compressor to work on them you need 32 units of industrial TNT!
To break it down, on top of the dust those three diamonds cost you 48 flint, 96 sand, and 120 gunpowder. Rubies require only three quarters of that figure to process, and I assume sapphires and emeralds match them, but frankly for the most part I'd consider it easier to just mine the quantities you need rather then setting up an infinite manufacturing line (assuming you want the actual gems).
At least as far as diamonds go I reckon fossiled bees are a better bet. Three diamonds out of them costs a lot more dust, but you only need 24 flint and 3 obsidian to get the same results - and a regular compressor instead of the implosion one.
My point still stands whether You think it important or not. There is No way IN ANY CONFIGURATION of pipes that you can tell when to pull out a serum, put a new one in, and refill the old one.
Why not just do what he suggested and time how long they've been in use? So long as your power supply is stable all you need to do is time it, and maybe count bees in/out.
Short of ComputerCraft, your system will have no way of magically reading your mind and figuring out that those bees you just threw in there need a humidity serum because you want to run them in a non-native biome. Hence you should always expect some level of manual involvement.
Oh, and
really "several days" for heroic bees?
How? Even without chunk loaders, that's a few hours idling tops, including setup. I'm really curious as to what took so long. Did you use minimum fertility and longest lifespan or some such?