Yes. There are some things not x64 ready (XojoScript for Example which is one of the reasons the ide itself is still 32Bit)
Also the Debugger (based on llvm) is not ready so thats why the button "run" get's disabled - you need to build x64 versions of your apps (at least for the moment) i think perhaps the debugger will ship with the next release of Xojo.
P.S. BTW, because of this I see that IDE recognize plugin only if it have 32-bit cocoa version.
-> That's a little out of my region of knowledge - perhaps there you will find better help from one of the other plugin developers (Christian Schmitz from Monkeybread Software for Example, or Einhugur Software - both of them have already updated most thier plugins for x64)
Problem is if i compile to x64 and cocoa_64 is not present the build process stop with an error. - so yes you would have to put all "supported" platforms inside the plugin - like Win x86, Win x64, Linux x86, Linux x64, (LinuxARM 32Bit), Mac x86 and Mac x64 - the IDE itself would use the 32bit file while design-time - and the 64Bit parts (and or other) only at build-time (for 64Bit)
I also don't know if it would still be possible with the old pluginformat (.rbx) or if you have to switch to the new (.xojo_plugin) format