In testing the modded mission files with 1.09, I'm finding that files which include new types added by mods are being merged in just fine, and those items are spawning.
However I have other files which modify vanilla types (for instance, setting the pliers quantity to '0', even though in vanilla types.xml it's set to spawn). This worked fine in 1.08, but I'm finding that 1.09 is ignoring these changes and using the vanilla types settings, regardless. This is also true with spawnabletypes.
I've double-checked my files, XML formatting, and paths in cfgeconomycore.xml, and everything looks good. It works fine in 1.08, as well. Can you have a look?