Suppressing unnecessary geometry will result in the Modal analysis taking less time to solve. That is all.

Turn off the automatic detection of contacts on Attach.  However, suppressing does not require a new Attach. Delete all the new contacts that were created.

Direct solving is best unless it is a very large model and you run out of RAM.

Two elements through the thickness is a Global setting.  It might cause your frequencies to move around a little because of a better quality mesh.