Because it's normal for big ships to be refitted when they're sufficiently old or when their primary tasks are changed?
But is it, when the E-nil is our only onscreen example of such an extensive refit?
As far as I know there's only one other example of a regular-duty ship being seen across multiple decades of service, and that's the Enterprise-D from the alternate ``All Good Things'' future ... which, of course, was prominently refitted.
Yeah, we see Excelsiors and Grissoms in Next Generation
that don't look too different from what they did in the movie era, but when we get interior shots they look like redressed versions of a Galaxy-class battle bridge at least. If (if!) they're three-quarters of a century old, they're not running the same gear they were when Genesis and Transwarp Drive were going concerns.