Do the dropdown search and replace lists work between sessions to be accessed?

Not totally sure what you mean, if you mean the dropdown lists on the entrys in the search/replace dialog get saved and restored when Geany is shutdown and restarted, then no.

Is v2.1 using a single colorschema folder for user and superuser?

There is the system colorscheme directory (usually /usr/share/geany/colorschemes/, or the same under /usr/local/ if you installed manually)

Or $prefix/geany/colorschemes if you built it somewhere else

Unrelated note: I advise against running Geany as root.

+100000000000000000000000000000000 Ubuntu (and descendents) broken sudo screws up which $home is used, so it depends on which distro you use what the answer to your question is, but its not different to 2.0 if thats what you mean.

Can I disable bracket highlights? Where?

See #3555

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