Sometimes, developers do not want some actions like copy/paste to appear in the toolbar, as the application looks too cluttered for example.
For Kate 3.0 (KDE 4.0) an up, indentation is scripted, that is you can write a javascript that can indent your files.
In the principle you can’t. Kate sees the document as a list of lines, and so far search and replace is done in one line at the time.