I recently accidentally upgraded a Colonizer into a Constructor by accident. Luckily it was an empty Colonizer (built at a Shipyard that wasn't close enough to any of the three sponsors) and was of more use as a Constructor; but that's beside the point. So, there's one predominant instance where better naming conventions would be nice.
There are actually Five parts to a proper name (due to the fact that it can also make a difference where the vessel was physically produced). The exact proper names for those parts might be the hardest thing to determine; but might I suggest:
Producer - The faction that originally produced the ship (two or three initials such as "TA" for Terran Alliance).
Make - The facility that produced the ship (again, two or three initials {or numbers if the shipyard is simply numbered and not named}); as it matters whether the ship was produced at a facility near a planet with Hyperian devices.
Model - Constructor, Colonizer, Freighter, Scout, Survey, etc.
Version - This is up to the designer: maybe it's the turn the design was made; or "Mk" followed by a one up number (or Roman numeral).
Number - Sequential one up number
The two most important for me (right now) are model and version; but the game is automatically adding the Maker ("TSS" and I'd rather it was simply "TA"; but that's just me).
I, myself, am currently using the following conventions in my vessel naming (within the designer); due to the limited space in the upgrade display:
SBC Mk III 27-2 would be a Terran Alliance StarBase Constructor with a speed of 3, movement range of 27 and visibility of 2.
I then rename the vessel to simply:
TA Constructor 01
As I don't (currently) need all the other info cluttering the display; since the game renames the ship with owner, the designer name, and a one up number (rather than the name I gave it). Personally, I think that once you rename a ship it should stay whatever you rename it and not be changed with an upgrade; as the details appear when you mouse over it (or click on it).
No, the purpose of the naming conventions I suggest (except for the Number, of course) are for use in the designer itself; unless the game is going to continue to rename my vessels when I upgrade. it's extremely cluttered right now and a better form of filtering and sorting would be nice. What better way than to adapt a naming convention at least similar to the one above?