Is there a way to determine the quality of MUF labled substrates?

If they've been kept reasonably carefully (dark/plastic jar, freezer or fridge as recommended by manufacturer) I've found that the substrates are a lot more stable than we think. Even if somewhat degraded, that degradation has likely released the MUF tag so you can detect that by measuring fluorescence of substrate solution. In terms of practicality, as long as your enzyme assays include substrate controls (the substrate alone - no sample) you can account for increased initial fluorescence of the substrate initially without major problems. I suppose you could have such serious degradation that your substrate concentrations are no longer in excess (so your reactions are substrate limited which brings up enzyme kinetics issues), but that's unlikely. You could buy purified b-glucosidase (etc.) and validate substrate quality by running assays using that pure enzyme, or just run a test set of samples (soil, water, litter) from anywhere. The b-glucosidase and NAGase you're assaying are common enzymes that you'll detect activity for in most environments.