Well, consider that the TARDIS is a living thing, and moreover one that is in love with the Doctor. She could always just throw herself into a sun or land on some remote asteroid, but that still leaves the chance (however small) that someone might run into her and remember.
To correct what appears to be an oversight, consider also what happens during "The Parting of the Ways" (or is it the one just before that?). The Doctor sends Rose home in the TARDIS and (by way of his answering machine), tells her to just leave it, essentially letting it die. His description of how it will be forgotten and ignored could explain why the existence of the Cowboy Hat Doctor's TARDIS isn't a big deal.
Additionally, does another TARDIS in the universe actually mess anything up? If you think about it, almost any time the Doctor does anything, there's at least one other Doctor out there with a corresponding TARDIS. Time travel does not lend itself well to avoiding multiples of oneself.