The process is called jumboisation, and evidently it's been pretty common for decades. Far more common with civilian ships than military ones, since the armor factor is a real pain in the ass for capital class ships. But it's entirely possible.
In some instances thsee refit improve the handling, such as changing the bow and making it better to handle rougher seas. Issues like stealth would be moot if this was done professionally. Now half-baked mods could take on all kinds of negative aspects. In the star wars universe they had fighter craft that were a combination of multiple types, basically whatever parts they could weld together. These had a definite deficiency against the front line X-wings and tie fighters, but they were deployed by peopLe who could not afford the real thing, or even the older, cheaper things.