Indeed it is, but it's hidden in SRB2DB, which in retrospect was not really necessary (it's in plain view in Workbench!). Hold Ctrl and Shift before bringing up the menu, and keep holding them while you click the "Find Identical Sectors" menu item (or whatever it's called).
The reason it's hidden, and the reason for the warning that it will give you, is that there are some obscure situations where merging identical sectors will potentially break special effects, namely those that rely on the global geometry of the sector. Things to be wary of are speed pads and certain sorts of moving FOF.