Same problems you have I had myself. Here is what I end up doing.

For bags I have a trunk bag with expandable side paniers. This is mostly empty, so I don't always need to use it. I take it in case I want to stop at a store on the way home. My laptop goes in a messanger bag. As others have said, I had no luck with paniers except in the front for touring, and these are not big enough for a laptop. I carry tools in an under seat wedge.

I carry my lock looped around the seat post (cable, not secure enough by itself), another one on the handle bars (u-lock style). When I lock up I remove the seat post with my tool bag. I figure it will be very hard to sell a Dahon without a 34mm seat post, and no Dahons in the area to steal said seat post from.