Is one's auto insurance deductible amount generally for each incident or accident that occurs or is it per policy year? If my comprehensive deductible is $1,000, does it make no sense to go through my insurance company for a cracked windshield?

Correct: If your deductible is 1,000.00 your replacement for your windshiled is between 2 and 400 (most likely) so just bite the bullet and pay it.
The other part of your question: Deductibles are for each incident. Wreck a car today, 1000.00
damage, youmust pay, wreck it again next week, and another 1,000.00 damage, you must pay.
You must be having a lots of accidents to have such a high deductible or did you choose that because of the rate. Be safe.