Indeed. A ship is a collection of those things. Which means you can probably replace most of the interior systems while still retaining the outer design.
Try using the case from a 1980's VCR to install the inner components of a 2013 BluRay player. See how that logic doesn't quite make sense?
It makes perfect sense, but not for the example you use. A couple of good examples would be the B-52 and the Space Shuttle. The B-52 is over 50 years old and is constantly being upgraded and retrofitted to extend its service life. Its purpose hasn't changed at all. As for the Space Shuttle, they basically ripped out the entire flight deck and installed brand-new computers and a glass cockpit, upgrading it over the '70s and '80s tech that was previously there.
Also, I visited the museum ship USS New Jersey (BB-62), which was commissioned in 1943, but was full of 1980s-era technology, so obviously they upgraded that ship quite a bit over the years.
I'm sure you can find other countless examples of aircraft and ships that have been upgraded over time, but you can't say that it's illogical.