Clear acrylic shoe boxes are your best bet here. They stack just like regular boxes but you can see exactly what's inside without opening them, and that alone saves you so much time. You can grab them pretty cheap online or at container stores. Get ones that are deep enough for your bulkier limited releases, and then use labels on the front or spine to mark brand and year - something like "Nike 2024" or "Jordan 2025." That way you can scan across your collection instantly.
For the actual organization, pick your system and stick with it. Most people go brand-first (all Nike together, then Adidas, etc.) with years inside that. Some do it the other way around, organizing by year and then brand within each year. Honestly either works fine as long as it makes sense to you. I'd say brand-first is easier because you're usually hunting for "where are my Jordans" rather than "what did I buy in 2025."
One thing that helps is taking a quick photo of your collection once you've got it organized, maybe a few shots from different angles. Sounds dorky but it's super useful if you're trying to remember what you have or checking if something's already in there before you buy it. Keep that photo on your phone. And if you're planning to keep collecting, leave some empty shelf space because at 45 pairs and growing, you'll be reorganizing again in a year or two.