Why Samuel Pepys could be corrupt and effective

Wouldn't it make sense for a corrupt minister also to be good with money?

Yes, within limits: Pepys was corrupt enough to benefit personally but not so corrupt that he stopped the administration doing what it needed to do.

The answer calls this the Pepys paradox. Samuel Pepys could participate in the patronage and corruption of his age while remaining effective at naval administration. The important boundary is whether private benefit obstructs the institution's necessary work. This makes it possible to understand Pepys without flattening him into either a disinterested reformer or a merely self-serving official.