Do you know how to use ahk (autohotkey)?
You could use something like this if so. Just compile the script and set it as the executable
#Persistent
RunWait, C:\path\to\Citra\Citra.exe,, Max ;Obviously you want to put your own path here. The Max arg should start the window maximized.
ExitApp
If there is a key combo to make the emu fullscreen, ahk could do that on launch also. I do not have this emu myself, but if you need more help let me know and I will download it and make a working script. I do recommend you have a look at the autohotkey forums. Autohotkey is an amazing tool when it comes to emulation.