I forgot to add the salt ingredient to a cookie dough that is already mixed. Is there still a way to add the salt?
At this point, I recommend skipping it. In the long run, it's not likely to "ruin" your cookies. It's usually just there for a bit of flavor enhancement, not likely for any chemical reason. There may be some slight difference in the importance of the salt depending on the type of cookie you're making, though. Something like a sugar cookie or chocolate chip isn't likely to need it much. A peanut butter cookie, though, the salt does a lot for the flavoring but if you use salted peanuts/peanut butter, there's probably already a good amount of salt in the ingredients, so you'll still probably be OK.
Mixing the salt with the flour is an important step in making sure it's distributed evenly. Once the dough is complete, getting the salt mixed in well would likely overwork the dough and give you tough cookies and even then, you may end up with salty pockets and some parts that are unsalted.
Many cookie doughs are pretty tolerant of over-mixing. You can just throw in the salt and give it a spin in the mixer. The salt won't be perfectly evenly distributed, but it should be good enough.
In fact... it's becoming trendy to put salt on top of things rather than mixing it all in. (Cf salted caramels). You use bigger salt crystals, to add crunch and textural contrast. It dissolves in your mouth, making for an interesting contrast of flavors.
So, if you've got some kosher salt or other fancy salt on hand, you could just bake them and sprinkle the salt on while they're still warm. (Use about 1.5-2x as much of a big fluffy salt as you would with ordinary table salt. Or just use plain table salt, if that's what you've got.) I often do this with bar cookies, sprinkling the salt right before they go in the oven.