It's pretty normal if you go at off-peak hours. At those times of day, the bottleneck in the drive-thru experience is usually the food prep and not the food vending. You can't get rid of the customer if the food isn't made yet, so taking the money while you're waiting for the food to get made isn't really too big of an issue, and it saves labor costs.I've seen one and two but I've never seen a McDonald's that has two windows and doesn't use both of them. If they don't it slows down the line to about double its time and would halve their income.
I think it can vary a fair bit from store to store and area to area as to the actual utilization of the 2nd window. I haven't worked there in 20 years, but I used to be a store manager at a McD's. High-volume stores (like $4 million+) can generally justify the use of it at all hours, but none of the stores in my franchise group were like that. We'd keep them both open during the peak meal rushes, but usually not during mid-day or during closing hours. And some stores, as @MysticMisty said, only ever used one. Mostly because they were built with the anticipation of doing $2.5 million in annual sales and only made $1.5 million. Note: I have no idea what current store revenues for a McDonald's are nowadays, but these were typical numbers for our area back then.
Another factor that can influence things is staffing. If you don't have enough employees to staff all parts of the store, you pick the positions that will create the least problems. It's usually the "least bad" choice that you've got.