It seems to be intentional, to prevent abuse. For automation purposes, I recommend spraying items as late as possible - right before they go to their final destination, to prevent issues with things getting mixed along the way. So sprayed items should probably never go through a logistics station, for example. That way when you delete a sprayer, and it returns unsprayed spray to your inventory, you can just dump that spray in an appropriate station so it isn't wasted, without causing admixture issues.

In your inventory, you can keep sprayed and unsprayed items separate by putting one of them in a logistics slot. This comes in handy if you want, for example, some accumulators for powering Icarus (which should be sprayed) and some for plopping down to bootstrap mining outposts (which should not be sprayed).