I have worked programming Twitter spam bots, and depending on your behaviour using the platform, it's like you build up a score, and when you reach a certain threshold, you get banned.
Everything that triggers a notification increases your score, and certainly favouriting tweets does so--but you have to be extra annoying for you to get banned doing this.
You can also get shadowbanned, which means your interactions trigger no notifications and your tweets simply disappear from everywhere. So if you're spamming you probably want to check every once in a while if your account is shadowbanned (by triggering a notification directed to a "control" account and seeing if it goes through) but there's no way to remove a shadowban: not even disabling/reenabling your account will remove it. It expires after a few days though.
There are "hard" rate limits in place as well (amount of favs/minute), but those can be avoided by using the API key of an official app. (Don't be mistaken--you build up a "spam" score anyway.)
I am hating this change a lot. I have been using the service for eight years now and the fact that a tweet started with @whatever was the visual indication that it was a reply. Now they have to ruin that too. I don't know, I sometimes feel like they are trying to piss me off or something.