Yep! (I got this info from the Ubi forum as I haven't done it in a while)
Go to your save game directory, usually "C:\Documents and Settings\yourname\My Documents\SH4\data\cfg\SaveGames\" and find the save game you wish to edit. This is easiest done if you just started a new campaign.
You might want to make backups of these files before you begin!
Open "Careertrack.upc" with notepad do a search and replace, search for the current boat name and replace with the new name. Save.
Open "ActiveUserPlayerUnits.UPC" with notepad and do the same.
[UserPlayerUnit 1]
ID=Porpoise
NameDisplayable=Porpoise
UnitName=USS Perch <<< rename the sub here
There should also be a folder called "UPCInitial" with the same two files inside of it. Edit those two files like above.
I think that gets it.
Please make backups before editing.