"Waste not, want not" is an idiom that has a specific meaning, but it is neither of the two meanings you suggested.
What it does mean, basically, is that if you do not waste that which you have (waste not), you will not later want that which you have wasted (want not).
The saying is meant to encourage those who waste resources not to do so, so that later when they look for resources, they will still have the unwasted resources at their disposal.
Edit: The confusion from the phrase "No pain, no gain" stems from the idea that the phrase "no pain, no gain" is negating both pain and gain. It is not. Both phrases mean that a lack of one thing leads to a lack of another. "No pain", as in if you do not suffer pain, "No gain" you will not gain anything. "Waste not" if you do not waste anything, "want not" you will not want anything.
The possible source for this confusion is the fact that the second half of the phrase, 'want not', implies having that which you need. But the phrase is "want not", meaning a lack of want (or need) for anything.