Using LR4 and a Mac:
1. My main drive shows I have 42,619 photos, however, I also see that on my Macintosh HD I have folders for 2001 with 9 photos, 2009 with 0 photos and a folder for 2012 with 1297 photos. All 3 of these folders have a question mark next to them. I have no idea why these folders are here, because I store all of my photos on the external drive with the 42,619 photos. When I expand these folders I get photos with question marks indicating the photos are offline. Any idea what might be going on with these 1297 photos?
2. Is there a way to search all of LR to find any missing photos/videos that somehow became unlinked/offline?
Possibly at some point in the past you imported photos to your main drive rather than the external drive, and then moved them using the Finder.
Regardless, the command Library > Find All Missing Photos will find all photos in the catalog that don't currently exist on the hard drive.