Previous Discover scans ran at a decent speed, but now the scans appear to be slowing down even though the amount of files, and data size are much lower than previous scans.

Is there potentially an issue I should look into?

If the option "None" is checked, then there may be errors in the scan.  Review the detection server logs or contact Technical Support for assistance.

If either of the other options is checked, the scan is operating in a differential mode.  In this mode, all files are checked to see if they meet the date requirements.  If they meet the date criteria they are processed and the file and data count is changed accordingly. 

Files that are not processed do not change the file and data counts.  However, there is processing done to determine if the file needs to be processed.  This work doesn't appear in the scan so it can appear that the scan is running slower.  The scan is working, it just appears slower because it isn't reporting the files that it has examined and decided not to process.