Absolutely . I'm working on stuff like that right now.
You can do it in two ways...
1) find Commanderblueprintsdefs.xml
.... Find the line that says hyperdrive plus.... Change it to warpdrive or just copy the whole line a few times.
2) find the commandercomponentsdefs.xml and add a speed boost ability to the admiral and Commander ship components.
Option 1 is much simpler and easier in my opinion.