Probably the same reason why Robert April ended up being Christopher Pike, Bill Ryker ended up being Will Riker, Beverly Crusher's daughter Leslie ended up being her son Wesley, etc. Early, rough ideas are just first drafts, and creators often think of something better later on and change their minds. We may never know the specific reasons why a creator decided Y worked better than X, but it's not uncommon. Sometimes there isn't a clear reason except that a writer or producer decided they liked the sound of one better than the other.
Although in this case, I would speculate that maybe Roddenberry or Herb Solow decided that "S.S. Yorktown
" was too specific to American history, and Enterprise
would be more universal. Although I'm not sure that's a good speculation, since they never seemed to have a problem with an American bias otherwise.
Perhaps it was that Enterprise
is a name with a more extensive historical pedigree, with more ships bearing the name. Perhaps it was chosen because the USS Enterprise
CVN-65, commissioned in 1961, was the first nuclear-powered aircraft carrier, so they thought it was fittingly futuristic/pioneering.