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The search field should be there. It's actually quite handy as a quick way to search recent history. If you set aside your preferences while OmniWeb isn't running does it start appearing?

1.) Quit OmniWeb.
2.) Move your preference file to a safe place (so you can place it back later to restore your settings).
--The file can be found here: ~/Library/Preferences/com.omnigroup.OmniWeb5.plist
3.) Launch OmniWeb.