Panama and the Central American coast have two seasons, not four: a dry season from roughly mid-December through mid-April, and a rainy "green season" from May through November. Afternoon downpours are typical during the wet months — often heavy but short-lived, clearing within an hour.
This is why the Panama Canal cruise calendar is so concentrated: full-transit, ocean-to-ocean itineraries are booked almost exclusively between October and April, with the dry season (mid-December to mid-April) considered the prime window. Very few ships attempt a full transit during the height of the green season.
The lock system itself operates rain or shine — a passing shower during the 8–10 hour transit won't disrupt the crossing. It's shore excursions at ports like Cartagena or Costa Rica that are more weather-sensitive during the wet months.