Red vs green jalapenos for canning
One difference you'll find is that the sauce is not as hot with the green jalapeños, because fully mature red ones have more capsaicin.  However, spiciness does not affect their preservation qualities.

Mature, red peppers have a slightly lower pH than green peppers(paper behind paywall, sorry) -- about 1.0 points lower.  However, both are still considered low-acid foods that require additional acidifying (usually using vinegar or lime juice in salsa) in order to be canned safely at atmospheric pressure.  I wouldn't expect the difference in pepper acidity to have much of an effect on the final recipe in a salsa that is primarily composed of tomatoes, so I wouldn't adjust the acid in the recipe.