Terok Nor is old and lived a hard life. I imagine its structure is riddled with micro fractures. You can only maintain and refurbish such structure defects so much, take it from an aerospace engineer.
Deep Space 9 isn't that old. Construction began in 2346 and finished in 2351 -- it's only about 37 years old as of the end of Plagues of Night
. By contrast, numerous Federation starships and starbases are actually much older than Deep Space 9 -- the entire run of Excelsior
- and Miranda
-class starships, for instance.