My grow bed is 12" deep, when making a bell siphon How much water level should be left at the bottom of the grow bed after the bell siphon drains the bed.
I don't think it really matters, since the roots won't really go down that far anyway, right? I also have a 12"-deep grow bed and a bell siphon. I cut the notches at the bottom of the bell siphon to be about a 1/2" in height, so presumably, the siphon stops sucking up the water at that height, thus leaving a constant half-inch or so at the bottom of bed. I doubt the roots will ever get down that far, but I could be wrong.
I have about 1 inch in mine. You don't need to worry about having it fully drain.
As a practical matter, I try to minimize the residual water. Most partical residue departs with the water. I drill 1/4" holes as close to the bottom of the bell as practical. When the siphon quits the bottom is only a wet surface.
I have about 1/8" left in one bed and about 1/4" in the other. Right now any solids are in the first 3" of the bed. Don't really think it makes much difference as long as the flow keeps it all moving around. I let the worms worry about anything left behind.
Seeing as the bed has water flowing in even when the siphon stops it isn't like the bottom of the bed will ever by dry.
Don't worry about it.
I have several beds that run constant flood and even many of my flood and drain beds have a reserve of water in the very bottom that doesn't drain.
Guess what, they all work. Some plants might prefer a particular method while other plants do better in another but to some extent it all works.
Now if you are really worried about getting the last dregs of water out of the bottom of the grow media you could do beds with false bottoms and set up your siphons externally so they will drain down below the bottom of the bed but that seems to be a lot of extra trouble and expense.
As to how deep roots will go. I have 24" deep beds and the roots of many plants will go right on down to the drains on those which are at the 20" deep level.