Hey Mori, welcome!
And yes, as you already know it does manage to get everywhere. So usually I say to take it apart and do it while bare, and then clean it out completely. But in reality you can do it either way, as long as you also block the vent bolt hole on top too. Might as well keep intrusion to a minimum.
You're not going to hurt the axle flanges, brake backing plates or the center section with blasting, and in fact having all those things clean and rust-free is a good thing anyway. But make sure you're going to be rebuilding literally everything, because the last place you want grit is inside the chunk and differential!
And even though the standard (sealed type) wheel bearings could care less if you have a little sand in the housing, if you're going to be upgrading to Set-20 bearings (tapered roller type) then grit in the housing is a complete no-no!
In the end, cleaning the housing should be easy and if you're having it put together by a pro shop, they should have the ability to flush out the housing anyway, before they put it together.
So I guess I'm torn on the subject. Can't say for sure one way is better than the other, so best to wait for those that have done it to chime in. And a lot of members have done that prior to powder coating, so you should have a good group of answers to cull from.
Just be aware though, that if you're going to be powder coating afterward and not just painting, then you are going to need to plan way ahead and make sure that your shock mounts are where you need them (disc brake kits often require moving them) AND that your pinion angle is going to be correct for what you're doing, so that you don't have to cut off and re-weld the perches on after the fact.
A few members have been there, done that too.
Good luck.
Paul