Nope, unfortunately you're probably stuck with both object names. Starting around Season 8, STO began automatically displaying the target reticule, name and all, around all interactable objects. There is presently no way to hide it.
Here's what you do. Split it into two objectives. The first is a reach marker objective around the ship called Locate the U.S.S. Myship. The second is your Scan the U.S.S. Myship. This puts the player in close range of the ship so they don't see the brackets for the invisible object.
With invisible objects I have started naming them with a punctuation, like a .
This allows me to keep the Distance to Target displayed, and the name is effectively not appearing
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Another trick you can do is use an enemy NPC Group (create it as a friendly faction so they don't attack and you can't attack) and set its end state (i.e., from visible to hidden) to THIS COMPONENT COMPLETE. Set your trigger settings as you wish.
Then set an on map Pop Up Dialogue whose initial state is set to WHEN COMPONENT COMPLETE and set it to the enemy NPC Group. Create at least 2 conversations in this dialogue tree.
Then create an NPC Contact, this is a duplicate of the ship you just scanned which disappeared and is meant to replace it. Set it's initial state to WHEN DIALOGUE PROMPT REACHED and select the second conversation box to the pop up above. This will make sure it doesn't spawn too quick but before the pop up box is gone.
NOTE: placement is key for this to work effectively so try to direct the player in a way where you are almost guaranted the ship they are going to scan is as directly in front of them as possible so the pop up dialogue will hide the ship. Because you are interacting with an object you will need to be a little closer than with an invisible object.
Like the rest of the suggestions it's not perfect but another option.