I just went through this decision process and decided on the propane bulkhead heater in my case, but I can certainly understand why other choices would make sense in other cases; there's some pretty decent products out there for each of the different fuel types.
A few factors that swayed me . . .
1) I have a propane locker in the back of a canoe stern boat and since it's advised to vent a diesel exhaust where there's no risk of it being below the waterline when heeled over, such as on the stern centerline, I couldn't run a hot exhaust pipe through the propane locker, so this was problematic.
2) For long range crusing, I didn't want to draw off the my diesel supply in case it's needed for running the engine. I can use 2 20lb propane tanks on my boat so I can use the LPG for heating / stove and reserve diesel for the engine.
3) I like propane for the reasons stated by others above, but also agree that the precautions mentioned are really important, such as having a fume detector and a CO detector, and also performing the leak checks frequently.
4) The cost of the propane bulkhead heater is significantly less than forced air diesel heaters.
5) The forced air diesel heaters use a bit more battery to run the blower.
6) The simulated fireplace is a nice touch.
These were some of my reasons, but I agree there's some offsetting benefits for some of the other options that can make another choice better depending on the boat, user requirements, and budget.
I agree the duel intake / exhaust pipe is a real plus for the bulkhead heaters, so there's little risk of consuming all the oxygen in the boat and/or having the exhaust become a problem inside.
I share the concern about the 3" hole required in the deck. I'm considering installing a larger deck place first, and installing the intake/exhaust pipe into that, so if I were ever in really dangerous seas, I'd have the option to remove the pipe and substitue the deck plate lid. I haven't thought this one all the way through yet though, so I'd be interested in any feedback anyone might have on a better approach. The concern about getting lines tangled around it can often be mitigated by a guard the vendor offers.