Hmm.
You should not have to set the signals as outputs for pre-synthesis signal tapping. I'd try turning on "Include subentities" just in case if for some reason the tool is thinking they are one level down.
I'd also try setting "Look in" to one level above with "Include subentities" turned on as well.
Post-fit nodes may not appear for a number of reasons using the post-fit filter, but anything in your code should show up with the pre-synthesis filter.
You don't say what version of Quartus this is, but you may also want to click "Customize" and make sure you haven't made adjustments to the pre-synthesis filter.