It won't have any effect on the bolts besides covering them with paint, but I imagine it'd be a huge PITA to mask everything off, and you're still likely to get overspray everywhere. Removing and replacing the cover is wicked easy, and it'll make painting it much less of a hassle. Plus, you'll get a chance to change you're differential fluid.
2006 LJ - 4.0L, NSG370, 31's
2001 XJ - 4.0L, AW4, 3.5" lift, 31's
1997 TJ - 2.5L, AX5, 2.5" lift, 32's - Sold
1983 CJ-5 - Stock - Sold
TJ Boot Camp