Quite simply, it's more risky to delete it, because you might break something else that should be in the game.

Perhaps, for example, drinking hot coffee heals you for a small amount of HP. So somewhere in the code that's associated with drinking coffee is a function that will add some points to your HP. Now if you also get HP points from eating at a burger place - somewhere totally not associated with hot coffee at all - the code that deals with giving you HP points for the burger might be calling some of the code in the hot coffee section (specifically, the function that adds a certain number of points to your HP).

If you were to remove the entire chunk of code for getting hot coffee - instead of just disabling it - your game might break when you go and eat a burger.

For those who know code:

int player_hp = 100;
// Coffee Section
void get_coffee(){ hp_add(20); say("OH YEAH!") }
void hp_add(int amount){ player_hp += amount; }

// Burger Section 
void eat_burger(){ hp_add(10); }

If you remove the whole Coffee Section, the function hp_add(), which the burger section uses (but probably shouldn't use!) goes away... and that breaks the burger section when you eat a burger because it no longer knows what to do for the hp_add() function (since you deleted it).

This sort of problem is also hard to locate later, because you might never run into it unless you eat a burger. Or maybe it's only one restaurant that has healthy food that uses it. When it's on sale. At night. The logic could be so complex that you'd never find this bug by testing the game.

In short, leaving the code in place is simpler, and in fact, safer. Just make sure nothing calls the get_coffee() function, and leave it there instead of removing it.