Quicker network with dual ethernet?
In all likelihood, the variation in speed you're seeing is happening due to congestion on your connection to the internet, not because of your home network setup. Even the Early 2005 Mac Minis could theoretically manage speeds of 12.5 MB/s, with a real-world throughput somewhere around 10 MB/s. The first Intel-based Mac Minis could handle 10x that.

Unless you notice the speed reliably changes based on whether or not you are connected over Thunderbolt, I'd assume the speed is actually varying because either the server you are downloading from is overloaded, or your internet connection is. If you're located in America, consider that at the hour you posted this, most people are going to bed, freeing up bandwidth for you to use.