How annoying do yo ufind the fan noise?
That's a very subjective question, of course. Personally, I don't find it to be a problem with mine (although to be fair, I've only run it ~ 1 hour so far, more to come this weekend if there is time). However, we have to consider a) my age and b) my experience. As you probably know, the high frequency response of human hearing tails off markedly early on in our lives. I and others simply won't hear to any real degree some high frequency components of that noise that you and others might, regardless of whether it can be measured by electronic equipment. And then I think life experience sets some expectations. I started my career working in labs with bank upon bank of diagnostic instrumentation that ran 24x7, bathing rooms in constant fan noise. I went on to spend nearly a decade working in data centres where fan noise, was and to this day remains, riotous. So I'm likely biased - nothing from this scope compares to what I've been accustomed to and so I just don't notice/care about it, perhaps.
All that said, I still don't think you will find it so bad as to be unworkable for you. It's louder that my old 2645B but much quieter than the Agilent I used to have. YMMV.
Consider also that if it does bother you, your environment might play a part in ultimately how much you perceive the noise. How you site it on your bench i.e. proximity to back wall, other objects, will have an effect on higher frequencies. It might be a case of adding some deadening material to your wall behind your desk/bench to cut down reflected noise, for example.
Did anyone come across details about changing the PWM settings via some Android hack? (Is it even confirmed that the fans are PWM-driven? How do we know if they are always on at full speed?)
I can't speak to how control has been implemented (I have no intention of opening mine) but there is control of some kind. There is a noticeable increase in fan speed during the boot process. Whether this translates to full scale speed can't be known without measurement but subjectively, it doesn't sound like it to me.