Is it better to close gates or save up clue tokens to seal them?
It depends. Mostly on how likely a gate is to open again at that particular location.

It's better to wait and seal gates with lots of gate mythos cards in the deck, to prevent them from continuously re-opening.

It's better to quickly close gates with few gate mythos cards and many clue mythos cards, as it will be unlikely to open again, and blocking access to valuable clues while it sits unaddressed.

The specific frequencies can be found in this document.