As with all things aviation, first honestly and accurately assess the mission, then the mod, part, a/c etc, then your own ability to fit those parameters.
People say funny things. Often what they say, and what they really mean does not quite line up. When someone says 'those really don't do much' what they usually mean is "I can't tell the difference", another often used mal alignment is 'those are not good' this often means " those add an attribute I am not comfortable with".
Furthermore, looking at some of the old threads (really old) that speak of inboarded flaps, it is important to note that they are just that... OLD. There are things that stand the test of time, as an example, in 1980 pulling back on the stick did the same thing as today.
But then there are examples that morph over time. For example, even up till 20 years ago, an O-360 cub just never would fly as sweet as a lighter O-320 cub. Haul a better load? yep, but for the simple fact that the only decent approved prop was the proverbial boat anchor at a station that was difficult to compensate for, they just didn't have a great feel. Today with all the uber light engine components and new prop choices, that situation has largely been diminished.
It sounds like you are in a position to either weld on a fuselage, or not. You didn't indicate whether you have flaps, or not, and if so whether they're extended or not.
I have flown the exact same cub for 10+/- years with stock flaps, and then another 10+/- with them inboarded. My experience is that they do just about what you'd expect adding another 7-8% of flaps to do.
The next time someone suggests that they don't do much, look over their airplane. With any luck one of their flight controls will have a 'trim tab', if so walk over and give one a sharp tweak for about a 1/2" and then plug your ears :lol:. When they regain their composure, explain that since they didn't see almost a square foot of added flap making any difference, you didn't see how a ity bity tweak could do any bad :lol:
My experience has been that most people that don't see any benefit, don't see it because they don't need it. They're fine and happy landing a touch faster or a touch tail lower.
As for the comments of negative attributes, I have not experienced any. My best guess there is once again what someone is saying is not jiving with what they really mean. Let me translate :lol:....
He said; "They make it fly poorly"
What he meant was; "I don't like how an airplane feels when it's all slowed up, and these let it fly slower" :lol: :roll: :lol:
Net Net, were it me (and it has been before, and will be again) I would not go out of my way to make an inferior wing. I certainly would not go through the effort to do it to a fresh cub I just bought with stock flaps, but the amount of work to do it when you are building up from a project is even less than negligible.
Lastly, mission frequently includes aesthetics, and that is a personal and valid point.
Take care, Rob