The best way to scan a print is to find the original negative and scan it instead. There is far more tonal information and resolution in a negative. The dark areas of a negative or slide hold much more information than a print. Dark areas can be brightened with a photo editor to bring out details that would not be visible in a print.
Beau Photos (near MEC) sells polyethylene sheet protectors that are designed for long term storage of prints and negatives. They fit into standard three ring binders and are useful for organizing too. But if you still have the negatives I would store them instead, and toss the prints. I have about 10,000 negatives on about two meters of shelf space. I don't keep prints.
Colour prints, slides, and negatives will deteriorate with time. The red layer is particularly sensitive toward UV and blue light. That is why old colour photos have an unrealistic hue.
Negatives and slides are made from gelatin which encourages mold especially in the presence of water vapour. Mold shows up as black spots that cannot be removed. If you are serious about long term storage, seal them in plastic and store in a freezer.
The most compact and convenient way to store photos is to scan them and store them in Adobe Lightroom.
The best way to eliminate dust and lint is to use a scanner equipped with digital-Ice. Scanners like that cost a bit more but use a IR beam to detect lint on the image and remove it automatically.
The scanner software can make a huge difference. I use VueScan ($39) instead of the generic software that comes with a scanner. I think they still have a 30-day free trial so you try before you buy.