When a compound is "pure" it means the contents of that compound are exactly what we claim them to be. If something is $99\%$ pure, that means $99\%$ of it is the expected material (in this case, meth), and 1% is other non-meth compounds.
Purity matters in chemistry and biology because the other compounds can be very nasty. In theory, if you had a bag of 100% pure meth, and a bag of $50\%$ pure meth, you could simply double the dose with the second bag and end up with the same amount of methamphetamine in your system. However, you would also have a double dose of $50\%$ "other" stuff.
Sometimes "other" stuff isn't a big deal. It all depends what that "other" stuff is. I don't know much about the methamphetamine trade, but the effect of purity is a big deal in the ethanol world. Moonshiners know to discard the "head" and the "tail" of the distilation, the first and last parts of the distilation, because they contain fusel oils (which taste really bad), and methanol (which can make you go blind in large enough dosages). They want very "pure" ethanol.
To you talk about the purity of prescription drugs, typically what matters more for the drug companies is that they fully understand what "other" things are in the pills or injections, and they are confident they are safe. That's why, when you look at many pill vials they will list their "inactive ingredients." They want to make sure you are very confident that the only things you are putting in your body are the "right" things. Going back to the alcohol industry, "pure" ethanol is actually $95.6\%$ ethanol by volume, and $4.4\%$ water. That is the limit for how "pure" ethanol can get with fractional distillation. To have ethanol in any higher percentages than that you have to go to exotic processes to create anhydrous alcohols. However, that is deemed "pure" because we still know what's in it. We know its $95.6\%$ ethanol and $4.4\%$ water.
Of course, $100\%$ purity isn't always the desire. There are myriad alcoholic spirits out there. All of them are sold at 80 proof ($40\%$ alcohol by volume), so they contain the same amount of ethanol. Its the "other" stuff that makes each spirit unique. You pay a great deal of money for the particular impurities that make a great well aged scotch. You pay very little for the impurities in a cheap tequila that leave your head pounding the next morning.