Is the deductible I pay for the Trillium Drug Program in Ontario considered a medical expense that I can deduct for my taxes?

Yes. This out-of-pocket expense can be claimed as a medical expense.

I just noticed however, that I deducted my prescription costs as a medical expense. Since what one pays to one's pharmacy via prescriptions is how the deductible is collected, then if I claimed 'a separate deductible,' I'd be claiming this amount twice. So I think if I've already claimed my prescriptions, then I've covered this.

You are correct - if you have already claimed these amounts as prescriptions, do not list the same expense.