If you do extended digestion times, you run the risk of essentially "shredding" the vector. No enzyme preparations are 100% pure. If one or more of the impurities cut the vector - either enzymatically or non-enzymatically - you run the risk of shredding it. I have seen that happen. Instead of getting nice crisp bands on your electrophoresis, you get the bands with smears. Worst case (and I have had that happen too) is the shredding is so bad that all you get is a "blob" at the bottom of the gel.

When doing digestions, you're going after the "goldilocks" time zone (not too short or not too long). If you are working with well known/characterized DNA the digestion times are well known. For other DNA, "trial and error" or empirical approach may be needed.