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We have applications that keep large amounts of idle connections (thoudsands). Does that hurt performance of the database? Is it worth it to lower the number idle connetions for performances sake?

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Not much.

Why are there thousands? Hundreds is reasonable.

Each connection takes some amount of RAM; if there are too many connections, you could run out of RAM, which would be bad for performance.

Also, if more than a few dozen connections suddenly get busy, they would be contending with each other for CPU, RAM, I/O, etc.

There is a "wait_timeout" that will disconnect a connection if it is idle for too long.

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