Fix term registration and non-theory-preprocessed terms in substitutions (#6080)

Fix term registration and non-theory-preprocessed terms in substitutions (#6080)

This fixes two issues for preprocessing:
(1) The term preregistration visitor was calling preRegister on terms multiple times in a SAT context, which the linear arithmetic solver is sensitive to.
(2) It was possible for non-preprocessed terms to appear in assertions if they were on the RHS of substitutions learned by non-clausal simplification, and substituted into assertions post-theory-preprocessing.

To fix (1), the SharedTermsVisitor is update to track which theories has preregistered each term, as is done in the PreRegisterVisitor. To fix (2), we no longer apply-subst after theory preprocessing.

These two fixes are required to fix #6071.

Note: we should performance test this on SMT-LIB.