There is a makefile called Makefile.in.in in the po directory that configure complains about.
So the makefile that reads "po/Makefile.in.in" must be named "po/Makefile.in".
After this change desmume configures and compiles fine under Linux Mint 13.
I don't know, if this is a plattform specific issue, but I think so. No need to do changes in makefiles or configure scripts. Renaming the file has done all the work.