So you still need filters, this not for the exhaust, but for the intake.
ICE air filter would destroy them in no time.
in one way it is a downside since its more parts and complication than maybe a pure EV architecture, but the similarities to ICE arch means that its an attractive option to transition to for both the OEMs and a tiered supply base used to working on ICE vehicles. If you can get economies of scale going and bring cost down for fuel cell its a great replacement for many (not all) ICE archs.
They are preferred solutions for larger vehicles because of the weight of lithium ion batteries. also because theyre optimized for power density while electric architectures excel with energy capacity/storage. But if you can implement infrastructure at the locations where these larger Class A vehicles are (or busses), then you dont care about capacity for the known universe's lightest (resting mass) fuel as much since H2 refuel times are fast.
You are correct about boats though, it is also a good solution set there. Planes will only work if we can achieve air cooled hydrogen fuel cells and eliminate the expensive and heavy balance of plant (Hysata).
Unless you burn the hydrogen, you aren't producing any emissions... unless you count water as an emission. Fuel cells don't produce any emissions.
Burning hydrogen though, does produce some emissions, however it's pretty minimal. I believe it's only NOx, and even then at far lower rates compared to gas vehicles. No CO2, CO, or any other stuff from gas or not-fully-burnt gas.
That said, I agree hydrogen has seemingly no place in something like buses. Frankly, the only places that I see hydrogen has any future is either going to be for planes and boats, or potentially for intermediate storage akin to batteries (i.e., create hydrogen with excess solar/wind power).