Why use Game Maker when you can use Unity? Unity 5 is now free and complete. The Game Maker business model is a joke and Construct 2 is able to create games 2d. Bad practices can impact performance but do not be obsessed with performance, it reminds me of the subjects' python vs ruby "or" java / c ". Start by mastering your tools and use those that suit your projects.
And keep in mind that the players targeted by your games are often equipped with PC ready to receive much larger production. For example minecraft has been developed in Java, I doubt that it was a choice regarding performance. The developer used the language with which he was most comfortable.