dnsmasq caches the hosts file so it's not that much an overhead. Anecdotally I've never had a problem with a 12k+ lines in hosts file (nor even several times that amount) on either Windows, FreeBSD nor Linux; and I certainly don't run powerful machines.
But that aside I wasn't suggesting that people run dnsmasq on their primary workstation. It's certainly an option, but I personally think it's better to have dnsmasq on a spare machine which is always on (doesn't need to be beefy, a Raspberry Pi would easily be more than capable). That way you can plum your dnsmasq IP into your DHCP server (or even use dnsmasq as your DHCP server as well) so that your phones, tablets and other devices all also benefit from ad blocking / tracking / etc.
Another option with dnsmasq is to run it directly on the router. Some consumer routers, such as Asus, allow you to access the device's command line via telnet / SSH. In the case of Asus, they literally just run dnsmasq for their DNS and DHCP daemons, so you could apply the hosts file directly on the router if you wished.