I want to block ads in my whole network with dnsmasq running on a Raspberry Pi, connected via Ethernet to the router. Is there any reason to take a RPi3? Or is a RPi2 also sufficient for that task?
An RPi2 is sufficient if your internet connection speed is less than 100mb/s which it is likely to be. If you have a faster internet connection speed then you would be better off with the latest model of RPi3 (model B+) which has an ethernet speed of about 300mb/s (gigabit port but speed is limited by USB 2 bus).
Having said that I would try to make the change on the router instead. I have DD-WRT installed on my router although I would recommend OpenWRT instead but either support dnsmasq modifications or even have specific services to block ads.