NOTATIO

I am having trouble placing the staccato (here saltando) above the invisible noteheads.
Should they be placed above the stem instead?

A matter of taste? I would center the dots above the stems.

Hm...
I think dots in the example above, look like they are off (not good).
If I put them over the stems than the first two dots are closer (not good). Than I need to compensate it by adding leading space for the second note (not good).

Gould actually handles this case on page 404 of her book with an example that is much like yours. She places the dots over the stems. It looks fine that way to me. She strikes a compromise in the spacing of the first and second "note" that is not objectionable.