This question comes up about every two weeks and the answers are usually the same. Those who believe it's ok to take out a seat do and those who think it's not don't. I don't think it's a good idea and eventually will show up with damage to the boat. I think the design and engineering community suffers from low esteem in the general public. Sometimes that's for good reason. I personally think automobile engineers ought to be chained to a car and be forced to make some basic reapirs under the hood. If they were I think some of their design decisions would be different in the future. We all know of examples where products might have been good or useful but for a bad design decision.
On the other hand, I'm going to assume that misguided or not, a designer or engineer knows more than I do about product development and manufacture. When considering whether or not to take out a seat I would urge you to take a look at the boat and how it was designed. Each manufacturer no doubt uses its best judgement as to how a boat should be built. I do think there are some design ideas that are common to most boats no matter who makes them. Please excuse my unscientific attempt below to point out a couple of important differences in how boats are made.
Both are made by Lowe. I couldn't find an exact counterpart of a riveted and welded boat and had to use ones as much the same size as I could. The boat on the left is a riveted L1648 and the one on the right is a RN1546 welded. I used screen captures so the resolution is poor but good enough to make the point. Note the difference in two areas. The ribs on the riveted boat are not as large nor do they go as high up the side of the boat as do the welded ones. Also, the gunnels on the riveted boat are not nearly as heavy duty as those of the welded boat. It is my belief that in both cases the reasons are that the welded boat was designed to be open and the riveted boat relies on the center seat for some of the structural integrity of the boat.
You can also see in the following two pics the differences between a boat designed to be open and one that relies on the center seat for its structure. I don't think the differences happen by accident and you can bet that the manufacturer isn't putting a dime's worth more material into the boat than is necessary .
I think most of us here aren't in a position to go out and get the thing we want but rather try to make the thing we have into what we want. Ideally we would envision the kind of boat we would like and go find one that fits the bill. I have a feeling it's generally the other way around. In the end I think it's important to consider what can reasonably be expected of the thing we've got and not try to make it into something it may not have been designed to be.
Short answer is no, I don't think you should take out the seat.