Yup - that's the Starfleet way, as we so readily witness. It may be different from how we'd do it today, but why should we know better then Starfleet? They are the professionals, the ones who'd be screwed if there really were some drawback to keeping the ship empty.
Fancy stuff happens. The Soviet high speed interceptor subs NATO called "Alpha", one of which menaced Alec Baldwin and Sean Connery in Red October, had to run their engines nonstop for ten years, even at the pier, or their power plants would have frozen solid - a weird arrangement that actually offered increased reactor lifespan and reduced fuel consumption. Old polar explorers in turn hoped to get frozen solid whole at anchor, the tighter, the better, as this best protected them from the elements. There's no real telling what pierside treatment is best for these cool starships whose "power regenerates" but whose fuel may blow up planets if accidentally released and whose waste products are handy for blowing up stars...
Timo Saloniemi