While reading Extending Sledgehammer with SMT solvers I read the following:
In the original Sledgehammer architecture, the available lemmas were rewritten to clause normal form using a naive application of distributive laws before the relevance filter was invoked. To avoid clausifying thousands of lemmas on each invocation, the clauses were kept in a cache. This design was technically incompatible with the (cache-unaware) smt method, and it was already unsatisfactory for ATPs, which include custom polynomial-time clausifiers.
My understanding of SMT so far is as follows: SMTs don't work over clauses. Instead, they try to build a model for the quantifier-free part of a problem. The search is refined by instantiating quantifiers according to some set of active terms. Thus, indeed no clausal form is needed for SMT solvers.
We rewrote the relevance filter so that it operates on arbitrary HOL formulas, trying to simulate the old behavior. To mimic the penalty associated with Skolem functions in the clause-based code, we keep track of polarities and detect quantifiers that give rise to Skolem functions.
What's the penalty associated with Skolem functions? I could understand they are not good for SMTs, but here it seems that they are bad for ATPs too...
First, SMT solvers do work over clauses and there is definitely some (non-naive) normalization internally (e.g., miniscoping). But you do not need to do the normalization before calling the SMT solver (especially, since it will be more naive and generate a larger number of clauses).
Anyway, Section 6.6.7 explains why skolemization was done on the Isabelle side. To summarize: it is not possible to introduce polymorphic constants in a proof in Isabelle; hence it must be done before starting the proof.
It seems likely that, when writing the paper, not changing the filtering lead to worse performance and, hence, the penalty was added. However, I tried to find the relevant code simulating clausification in Sledgehammer, so I don't believe that this happens anymore.