Easiest way (short of simply ignoring the warning) is to declare your sections twice:
segment Mydata public use32 class=data
segment Mydata
...now your section still has the "attributes" you declared on it, but the _SECT_ macro (used by the "struc" macro) isn't lugging them around, and Nasm doesn't delude itself that you're trying to change them. (if you were *actually* trying to change them, it *would* be an error!)
The other way would be to use the "xstruc" macros, available in the "contributions" package, instead of the built-in "struc". They don't use _SECT_, and shouldn't cause the problem. (so I'm told - haven't actually used 'em)
You can put "bits 32" at the beginning of the file (-f obj defaults to 16-bit), which will at least make the "default" section 32-bits - shuts up the linker's complaining about the 16-bit section, but you still get a section you don't want or need...
I just declare the sections twice, if I run into it.
Best,
Frank