On average the Complete Scan should usually take around 30 minutes to scan the database and every file on the site (except for files on the exclude list). On a simple site with an optimum host it could take 10 minutes or less, and on big sites with lots of plugins and extra files it can easily take an hour or more. There are many reasons that could cause the scan to run slow but I have found that if the scan takes more than an hour there is usually a simple fix that will speed it up depending on the primary cause of the slowness. One easy thing to try would be to increase the memory_limit in your php.ini file (the more memory you allocate to each PHP process, the more likely that each process will complete quickly). You might also check the scan results for Read Errors that have caused the scan to get stuck on various files throughout the scan, figure out what caused the error and the scan continue at normal speed. You can also delete any inactive plugins and themes, clear all cache, and delete all unneeded files from the site to lighten the workload for the scan.
If you need more help figuring out what is causing the slowness you can send me some screenshots of the scan at various points throughout so that I can get an idea of the general progress and scan stats.
