Do bases dissociate in acids and why?

First I need to clarify what you're talking about.

Many drugs are either acidic in nature or are salts that are paired with acids (alkaloids paired with an HCl molecule, for example).  Some of these substances may be broken down in the stomach, but most of the medically relevant ones do not.  Simply being acidic or an acid salt doesn't mean a substance will or will not be metabolized in any particular part of the body.

With respect to simple chemistry, acids and bases will react with each other to form a salt.  Sodium hydroxide and hydrochloric acid, both corrosive and noxious substances, pair to form table salt - relatively innocuous.

If you were to ingest a mildly basic substance - like baking soda - the sodium bicarbonate will dissociate in your stomach to sodium and bicarbonate ions, which will react with the hydrochloric acid naturally present in your stomach, neutralizing the acid and the base.

To explain this further, I'd need to know more about what you're asking.  Hope this topical explanation helps.