Just because there are cracks in the caulking doesn't mean it will leak when it rains. The crack may not go completely through the caulk. There should also be a layer of putty or butyl under the seam that the caulk is protecting.
Cracks in the caulk become a problem when there are gaps or there is no butyl putty in a seam or when the crack is allowed to collect moisture and go through enough expansion/contraction cycles to open the seam.
With that said, it's always best to re-caulk at the first sign of cracking.