With newer slide films and the current trend to put minimal markings on mounts, this can be an issue.
I use VueScan, and if the preview looks backwards, I simply click the "mirror" button before scanning. With a Plustek scanner, I have not noticed any difference in quality when the slide are scanned backwards.
If you can identify the emulsion side and be consistent with that, it is helpful. Not long ago, I was reviewing scans from slides I had taken during a college trip to Europe in 1982. I used the location of cars on the street to help orient the scans. Unfortunately, I had initially confused the locations of the photographs and put French cars on the left and English cars on the right.