I go with upgrading the tonnage first, then adding slips once I reach a target tonnage. The main reason for this is the time to upgrade 50 tons capacity (1 hull size) is multiplied by the number of slips you already have. The time to add a slip however is just based on the tonnage that can be built. It takes the same time to add 1 slip to a 3 slip shipyard compared to a 10 slip shipyard. It would take 3 1/3 times as long to add that 50 tons capacity to a shipyard that has 10 slips on it as compared to one with 3 slips.
This is not cast in stone, but once I pick a general size for a ship class I tend to stay fairly close to that size. If I later decide a need a few more tons capacity, that is not to hard to upgrade to. A major upgrade of size is generally not needed. I also tend to cap any one shipyard at the point of having 3, 5, or 10 slips. 3 for quick to make ships that I won't want tons of, these are generally specialist type ships. 5 slips for most ship types, and 10 slips for ships I will make a lot of, this includes freighters, light combat/patrol ships, surveyors, ect.
Brian