Can you please tell me more about your BDs?
Where does the water go once it goes through the BD? Do they clog? Trap fish?
I have Koi Toilet bottom drains with the built-in aerators. There are lots of other options. If you get one 4" drain I would recommend something like the Rhino II because of the integrated check valve for the air.
There are various ways to plumb the bottom drain but something like the bottom drain to a Nexus 320 or an Eazy Pod Complete with the pump AFTER that is a fairly complete filtration solution. The water is pulled through the filter by the pump and is then pushed up to the waterfall. Other people use a settlement tank but I don't have personal experience with that so I cannot weigh in on that.
My drains have a 3/4" gap meaning only something that small would be able to get sucked up the drain. I have no fish small enough for that to be a concern. As for clogging, it's pretty hard to clog a 4" pipe. I'm assuming you would also have a skimmer to catch leaves or other surface debris and you'd have things situated to prevent rocks and/or gravel from falling into the water.
There are videos on YouTube showing the installation. My favorite is the pond construction series from The Pond Digger. It has step-by-step instructions for the bottom drains as well as just about every other aspect of building a liner pond.
This is a garden pond forum so under no circumstances am I "judging" anyone who doesn't have a bottom drain or who has gone years without needing one. If you are planning on, say, 10 total pounds of Koi in a 4000 gallon pond then you're really not talking about a lot of waste. But if you have 50+ pounds of Koi in that same space it's a different challenge altogether. The koi poop has to go somewhere and having it settle on the bottom having to be manually vacuumed out is a maintenance challenge. I say this as one who did that every other day for a year. If you are starting a new pond rather than working with an existing pond, now is the time to install a bottom drain if you're ever going to have one.