I do not think most people have that many chargers. I have kids, each with their own systems and chargers, plus mine, plus a spare from some old system (dsi maybe?)
But yes, MOST people buying a n3dsxl do have at least 1.
And as far as trading it in with their old system... it's not Nintendo's problem. It's also only a requirement to include the charger when dealing with a big chain like GameStop. So maybe just use craigslist or ebay or any other number of avenues with which you can sell an unwanted electronic.
And I'm not saying electronic waste is priority for Nintendo. In fact, I doubt they even considered it (well, I'm sure some numbers guy somewhere factored it into some spreadsheet somewhere). But the fact is, whatever their motivations may be, it does reduce waste.