Ermm... could it also be that weapon upgrades for guns make them more reliable?

Anyway, i wouldn't sweat this little detail too much. Seems to me that the enemy could keep the guns dry inside the castle walls or under protection until it was time to fire them. I would suggest that you try a custom battle without the castle assault in heavy rain and see if your muskets fire.

In fact, i'm off to try that now...

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"You have offended my family, and you have offended a Shaolin temple."