Ammonia is also a product of the fish breathing. So no, vacuuming the bottom of the pond will not help. It might reduce it if you vacuumed every day, but as long as the fish are alive, there will be ammonia.
The beneficial bacteria in your filtration system, or on hard surfaces in your pond, is what keeps the ammonia in check, converting the ammonia to nitrite, and converting that to nitrate. That is the nitrogen cycle and it is constant and never stops. So having sufficient bacteria and filtration is critical.
What kind of fish do you have? And how much filtration are your canister filters rated for? It's normal for that amount to be overrated, or rated for a pond with no fish in it. It's always good to have way more filtration than what is rated for the size of your pond. The more, the better.
Is your pond new? If so, the bacteria may not have had time to grow enough to handle the amount of ammonia in your pond.
Please read about the nitrogen cycle and you will get a better understanding of the process and what is needed for a healthy pond.