I personally think that Shinki is more powerful than Hecatia, though her win wouldn't be an easy one by any margin. The fact that Hecatia has the three most prominent hells under her sway (aside from any lesser ones) proves she's up there in the high echelons, but Shinki is greater as a creation god than Hecatia.

Besides, when it comes to Alice you just don't piss Shinki off... as a certain shrine maiden came to realize.

Hecatia is already stated by ZUN in Strange Creators of Outer World vol 1, to be the most powerful character in Touhou. Shinki also hasn't even been confirmed canon in the windows era touhou games nor has she made any appearances in anything official. So it's hard to say a character that technically doesn't even exist anymore is stronger than one ZUN himself said is the strongest of them all.