The cleaner the water the better, but a little pollen in the water shouldn't hurt your horses. Horses are tougher than people give them credit for. They don't need perfect water all the time.

If you need some help keeping your water trough clean, put some fish in it. You can use those algae eaters (plecostamous) or goldfish (I prefer the plecos personally). They can have a hard time adjusting to the water so you'll have to buy like 10 or 12 of them and then maybe 2 or 3 will make it. And you have to take them out in the winter before the water gets too cold but it's kind of fun to have fish in the water trough.

Pollen isn't hard on a horse, they're out in it every day...clean your tank as many times as it takes to keep it relatively clean..if that's three or four times a week due to either dust, hay droppings into the water or whatever then you'll need to do it.

I like my guys to have clean water. I fill the tank 2/3 of the way and when it's almost empty I swish it around then dump and rinse.
If the sides of the tank are slippery when I slide my fingers across I will take a brush to it and a 'glug' of bleach...rinsing well after.

I keep my water tank under the run-in so it's out of the sun and blowing dust and the pollen.
Pollen won't hurt but sure does mess up a tank!