Get it caulked now and ask the handyman if he detects any damage.

We bought our home 3 years ago and made the unpleasant discovery that during severe storms water would seep in around the windows on the southern side of the house, and accumulate on the sills. After a few times I decided to call a handyman to caulk around the windows... next time it happens. I kept procrastinating, and then it just stopped happening. For example, the storms last night were very severe, and no water seeped in. No more water in the house! Yay! But now I'm thinking... this issue is not fixed. The water may not be coming into the house's interior, but could it be seeping in between the siding and the rest of the house? Could it cause damage that way? I don't know, and I'm looking for suggestions/insights. TIA!