Can an instrument that only appears in one spot be removed from the rest of the score?

If you only want one instrument hidden when it's empty you can right click the staff, choose staff/part properties and set "Hide when empty" to "Always" and only that staff will always be hidden when it's empty regardless of the "Hide empty staves setting" in Style...

If you want to add a note to a hidden empty staff you actually can. Select a note on the staff above it and press Alt+down arrow or on the staff below it and press Alt+up arrow (you made need to press Alt+arrow more than once). You can then add notes to the hidden empty staff. Hint, in version 3.5 (probably in some earlier versions too) the status bar tells you the long name of the staff the cursor is currently on so you'll know if you have the correct staff. Give it a try, if you're wrong then undo it. And adding a note will unhide the staff on that system.