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I use DevonThink myself. The desktop version is awesome. But the iPhone/iPad version DevonThink To Go is mostly used as a reader app. IMHO DevonThink To Go needs a lot of work. There is no cloud sync solution for DevonThink. You can connect your iOS device to your Mac and then sync documents to DevonThink To Go that way but there is no cloud access.

I've seen some people use Evernote as a file reference because it is a cloud solution. Documents are stored on the cloud to enable ubiquitous access to your files from anywhere.

Maybe you can create a context called "Notes" and set the context's status to "On Hold" (control-click on a context and select "On Hold"). This should keep your notes hidden from active context view but you can still see it in project mode.

I usually don't like mixing my notes with my tasks.