normally a failed compressor won't cause the clutch circuit to become overloaded and "pop" the fuse.
The clutch only draws so much amperage regardless of how much mechanical load is placed on the clutch. If the compressor is bad, generally speaking one of a few things will happen. One, it'll seize and smoke the belt. Two, the a/c won't work. And three, the entire system will be full of failed compressor material, negating a complete system replacement in order to do the job correctly so that it will last. Otherwise you're taking a chance of repeating replacement of expensive components.
IIRC your tractor uses a scroll-type compressor. Very efficient design. BUT they are not bulletproof. If anything they're slightly more sensitive to moisture in the system and high temp and pressure. So, if the screen and/or condenser are run for a long time being plugged with chaff, the compressor will run hotter than it's designed to, as well as higher pressure than it's designed to, and over time will eat itself.
Anyway back to the topic of blowed fuses. Yeah I'm from the South, I say "blowed". The fuse is seeing excessive amp draw through it's circuit, which causes the element inside the fuse to melt. But therein lies the question why is it getting so much current through it? You have stated that it will run a while before it pops the fuse, that tells me that the liklihood of a shorted circuit is low. Thus, the next most plausible theory would be that of a component or conductor that is either (1) intermittently shorting to ground (or Kubota calls it "earth") or (2) a component or conductor is corroded, or whatever, causing higher resistance, leading to an overheated circuit.
So what I would do in a situation such as this is to grab your wsm, and look at the a/c circuit. Find the fuse in the wiring diagram and follow where the wires go. One side will end up at battery voltage. The other end, however, may feed the fan, compressor clutch, switch, whatever. Every one of those components in the fused circuit are then a potential culprit.
I find it best to grab a piece of paper, and write down the possibilities, then eliminate them via testing one by one, and don't forget to test the conductors (wires) as well. At some point you will figure it out.