Actually, barrel droop IS something done intentionally by some manufacturers. It's a left over from the days before scopes became so common, and had something to do with the geometry of open sights and low powered guns. No one knows why some companys (Diana aka RWS comes to mind) still insist on doing it. In Greg's case, it wasn't droop, but a manufacturing flaw. Same effect, different thing. And in your case, it's probably a non-issue.
That said, I had a CFX with droop, but an adjustable mount or shims solved the problem. The way to tell if it's an issue is to make sure your scope is optically centered. Another new term? It simply means that your windage and elevation adjustments are centered, so your scope has it's full adjustment range available. I beleive there are a couple of good articles on optically centering scopes in the Library. And despite popular opinion to the contrary, counting clicks both ways is NOT the proper way to do it! Once the scope is centered, mount it and shoot at a target about 10 FEET away. Check point of impact against point of aim. POI should be about the same distance below POA as your barrel centerline is below your scope center line. Remember, small differences matter here. One MOA at 10 feet is only .03 inches. A typical scope has 1/4 MOA clicks. At 100 yards, that's approx. 4 clicks to move 1 inch. At 10 feet, that same inch will take over 130 clicks! If you have more questions on this subject and can't find the info, feel free to email me direct.
To get back to your original question, droop won't have an impact on leveling your scope to your rifle. I think most guys are like me, we just eyeball it. For the shooting most of us do, and the ranges we do it at, this is probably good enough. If you want or need more precision, there are tools that will help. Just check the various suppliers for scope mounting accesories. And if you have more questions, just post them :-)!
Dave