I would guess that the terminology goes back to the work of Sullivan and Quillen on rational homotopy theory. You should probably also look at the paper of Deligne-Griffiths-Morgan-SullivanDeligne-Griffiths-Morgan-Sullivan on the real homotopy theory of Kähler manifolds. Actually, I think that at least some familiarity with the DGMS paper is an important prerequisite for understanding many of Kontsevich's papers.
In the context of rational homotopy theory, I think the term "formal" is fine, for the reasons I've explained above. Perhaps in the more general context of dg algebras, the use of the term "formal" makes less sense. However, I think that it is still reasonable, for the following reasons. Let me use the more "modern" language of A-infinity algebras. In general, it is not true that a dg algebra $(A,d)$ is quasi-isomorphic to $H^\ast(A,d)$ considered as a dg algebra with zero differential. However, it is a "standard" fact (Kontsevich-Soibelman call this the "homological perturbation lemma" (for example, it's buried somewhere in this paperthis paper), and you can find it in the operads literature as the "transfer theorem") that you can put an A-infinity structure on $H^\ast(A,d)$ which makes $A$ and $H^\ast(A,d)$ quasi-isomorphic as A-infinity algebras. The A-infinity structure manifests itself as a series of $n$-ary products satisfying various compatibilities. Intuitively at least, these $n$-ary products should be thought of as being analogous to Massey products in topology. So $H^\ast(A,d)$ with this A-infinity structure does carry some "homotopy theoretic" information. In this language then, a dg algebra $(A,d)$ is formal if it is quasi-isomorphic, as an A-infinity algebra, to $H^\ast(A,d)$ with all higher products zero. In other words, all of the "Massey products" vanish*, and thus the only remaining "homotopy theoretic" information is that coming from the ordinary ring structure on $H^\ast(A,d)$.