Will I regain resources by deconstructing my base?
The short answer is: Yes. You do, in fact, get the resources back from deconstruction.
If you want to deconstruct a Seabase module, equip the Habitat Builder and hold "E" while facing the module. The materials used to create the module will be returned to your Inventory.
Source
This is often always the best option, because it is fairly easy to run out of resources such as quartz. Once this happens, you must either brave the deep, deep caves for more, or deconstruct existing structures to regain resources.