I'm searching for a way to freeze/delete definition queries of several layers at once (instead of doing it manually by opening the properties of each layer). I'm working on a SDE 9.3.1 Geodatabase.
I assume you mean definition queries of layers in an ArcMap document. In that case, the source database isn't an issue, it's a just a property of the layer object in the map. There's no way (I know of) in the GUI of ArcMap to do it. You could program a tool that could loop through all the layer objects and clear that property. (Not sure what you mean by freeze.) Which means understanding the ArcObjects references involved. And if you want it to work when you go to 10, VBA is out.