Scrapers usually add the correct name (if detected) to the EmulationStation's gamelist. The internal EmulationStation's scraper does use the file name for search, if your file names don't match what data exists on the scraping sites (TheGamesDB or Screenscraper), you'll get no matches. If your ROM files follow No-Intro naming convention, most of them should get detected (homebrews/custom ROMs will have the most issues).

You can use an external scraper that looks at the contents of the ROMs - instead of using just the file name. Look into using ARRM, Skraper or Skyscraper.

If you still need want to rename your ROMs, a ROM manager like 'CLRMamePro' or 'RomCenter' will probably do that, but that's a bit more complicated than using one of the scrapers mentioned above.