Well, it certainly means it has fewer options on it. So, yes, the purchase price when new was lower than a fully loaded model.
If you intend to drive it for a long time, I would suggest that a model without power windows is a better choice. This goes for all options that you don't really need. It's just one more thing to break and cost a lot to fix. I've always driven older cars, and I prefer base models with few options.