Heh, I was just getting ready to point out that in one of the pics in the article (and the MS blog post it links to as well,) you can see the "guts" of the datacenter, including regular air-fans to circulate the air in the pressure vessel.

More likely, for clearing the intake / outflows, they'd use an ROV rather than an autonomous robot, if only to reduce the chance of an accident and have a better chance to deal with something unexpected (like a not-so-friendly octopus making it's home over the outflow.)  If I recall right, as well, the unit is only ~100-150 feet down which is well within sport diving (to say nothing of professional diving) limits.  In which case they could hire a local diver to go down once a month with a crowbar to clear off the intake and outflow, probably for less than an ROV would run.