You can get rid of this popup by always using the same exact name for your swatches that have the same color recipe UNLESS you're using a different color or a modified Pantones.
It's a good practice to keep your swatch names well identified anyway if you do a print job and also for future reference.
If you use Pantones as spot colors, try to always select either Pantone coacted (C) or Pantone uncoated (U), make sure you use "book color".
If you modify your Pantones to CMYK, rename them in your own way by adding some extra words to define them clearly, for example "pantone 485-cmyk". Don't forget to also put that color in "process color", and not "spot".
If you modify the recipe of your color to a custom one, then a good thing to do is to rename the color like this "red-50-100-100-0" or simply "50-100-100-0". This way you also have a quick way to know what recipe you previously used without having to open each swatch to verify!
If after doing these things you still have that message, you'll know you can safely "merge" your swatches.
You can rename your swatches by double-clicking on each of them. Keep your swatches clean and sorted. Doing a "select unused" and deleting them can also help to get rid of the clutter! It's a good thing to do this at the end of your project at least and verify if you have some duplicate.
Edited: Frankly, I don't do "stylesheet" in Illustrator, but in InDesign you have this setting you can change in your preferences if that ever becomes an issue on this level. I really don't recommend it, it's better and easier to be more "disciplined" with your swatch colors!