The short answer is no. Whatever thickness the sauce is when it goes in the jar is what it will be when finished.
I am curious though why you cook the salsa for six hours? Salsa is typically a fresh product. If you cook it for six hours isn't that tomato sauce?
Before I forget, some watery products like your salsa may appear to have separated after you water bath them. This is normal. Sometimes the solids will float a bit, leaving a watery appearance on the bottom. Nothing to worry about. When you open the jar, give it a short stir, if necessary.
Are you pressure canning your salsa? Salsa is one of those foods that really lie on the edge of being safe, canned with a traditional water bath canning method. All the other ingredients that you add to the tomatoes can take it below the acidity level where you don't have to worry about botulism. Now I admit that I do can salsa using just a regular water bath and have never had a problem. It is a very slim chance but it is something worth noting as Botulism is not anything you want to mess with. In recent years I've taken to adding some vinegar to my canned salsa to ensure safety.
Watery salsa comes from a variety of reasons. First off, when making salsa I usually use paste tomatoes (romas) not regular tomatoes, or at least a mix of tomatoes, heavy on paste tomatoes. I also remove all the seeds, along with the watery gel that they come in. Finally I usually also add a bit of tomato paste to help thicken my salsa. I usually cook my salsa for about 45 minutes to 1 hour then blend it. For canned salsa I like a thick, slightly smoother salsa similar to what you would get a Mexican restaurants. I also char my tomatoes and peppers, on the grill and grill the onions before putting it all in a pot to cook. I also don't skin the peppers or tomatoes as I want that char in my salsa. If I'm making fresh then I usually just make Pico de Gallo.
Romas tomatoes is a great tip. I will make my next batch with the Romas tomatoes. I will also squeeze the tomatoes to remove the excess water. First batch ever.. I reduced this batch and drained a bit. It is so far working out. Thanks for your informative response.