Yes fish can go through. I have a 10" pipe in my Agri-drain box and have seen lots of fish go through it with the standard inlet trash guard. Screening off the inlet is risky because it can become plugged. Taking water from the bottom is a good idea. All of these things have been stated here already and I just want to "plus 1" these statements because they are spot on.

Let me add two things. First taking water from the bottom may cause problems if there is a lot of sediment. Try to stay a foot or so off the bottom so you are not sucking in sediment. Secondly if you try to screen off your inlet pipe make a large box around your inlet. The more surface the box has the less chance of plugging up.

Lastly Agri-drain does make a fish screen that fits in the box but I have not used one yet. My ponds are weedy and I think it would just plug up.