Has the compactness theorem for FOL been formalized in Coq/Isabelle/etc?
The compactness theorem for classical first-order logic is a direct consequence of the completeness theorem, and, actually, one can prove directly Compactness by the Henkin-style argument used for Completeness without ever mentioning derivation.

The Completeness theorem for classical FOL with respect to standard Tarski models has been formalized in Mizar. See the series of articles under http://fm.mizar.org/2005-13/fm13-1.html

The same completeness theorem, but with a constructive proof, has been almost formalized in the Coq proof assistant by myself, see the zip file under https://sites.google.com/site/dankoilik/publications/phd-thesis

I say "almost" because there is one technical point, proving a correctness of a sorting algorithm, that I have not yet had time to finish, however the main ingredient (constructive ultra-filter theorem for countable languages) is formalized.

One can also consider Completeness, and hence Compactness, for a non-standard notion of validity, and get a complete and formalized constructive proof.