I do it all the time on the 60 but I haven't built a 40 in several years and don't recall a lot about it. I know I removed a bay but can't recall how many. I use the 60 to teach building and have made mods with almost every one. Last one I did was last year and it was with an older fellow and left completely stock.
Two bays on the 60 really helps with the roll rate and doesn't seem to harm the floating of the plane at all. They do have a huge wing on them and I understand they are still a trainer but two bays on the 60 works just fine. The 40???