Dynamic programming is, almost by definition, to find a shortest/longest path on an implicit dag.
Every DP algorithm just does this.
An Holographic algorithm can be loosely described as something that counts perfect matchings in implicit planar graphs.
So, my question is: are there any other families of algorithms that use well-known algorithms over implicit graphs to achieve a considerable speedup?
Optimisation problems for which a greedy algorithm always gives an optimal solution have matroid structure. A matroid is a set system, so it’s more general than a graph (which is a set system in which the subsets (called edges) all have exactly 2 elements) but it might still be of interest to you.
Holographic algorithms look very interesting and I haven’t heard of them before — will definitely take a look!