Although there is a certain sense in which universal algebra is a subfield of model theory, people in the two fields are interested in very different things.
Nevertheless, I understand that universal algebraists sometimes talk about ultraproducts. This suggests to me that full first-order theories of structures are sometimes useful in study of their equational theories; if not, the could just use products since they preserve equations (but not necessarily first-order properties). But I fail to see how they are useful. Skimming the last chapter of Burris and Sankappanavar did not quite help me.
How can full theories of structures be useful in study of their equational theories?
Every equational theory is a first-order theory, so, at the very least, universal algebraists should be able to use the ultraproduct.
You ask why would they would need the ultraproduct when the product preserves all equations. In general, one could make the claim that universal algebraists tend to care about finite structures whereas model theorists prefer infinite structures (again, this is a generalization). The ultraproduct construction breaks down with finite structures:
If $\mathcal{K}$ is a finite set of finite algebras, then any ultraproduct of algebras from $\mathcal{K}$ is again in $\mathcal{K}$.
However, a product of algebras from $\mathcal{K}$ can be made arbitrarily large.
Two nice results that use ultraproducts in this way are a result of Jonsson, which states that a finitely-generated congruence-distributive variety is residually small, and a result of Quackenbush, which states that if a locally finite variety has only finitely many finite subdirectly irreducible algebras, then it cannot have any infinite subdirectly irreducibles.