Same issue here. This has been around since 2014 (see https://forum.affinity.serif.com/index.php?/topic/452-pixel-snapping/) and still isn't properly implemented.
Meanwhile it's 2018 and I'm getting this (this is a part of Grade UI pack, which everyone who has Affinity can grab):
Just moved the top box, with with pixel snapping turned on, without snapping override (Alt-key). Fraction coordinates, blurred artwork. When is this going to be fixed? As in: working? When preparing this screenshot I drew an artboard to export this part of the file. Guess what: despite pixel snapping the artboard got a half-pixel height. FFS.
I paid for both Affinity apps and even got my company to buy another copy of Designer. I get to read a flurry of posts about yet another platform releases, awards of the year, how Affinity can replace Adobe apps, whereas basic stuff like this still causes trouble.