Whether or not you have margins probably depends on the style of portfolio you want it to be. Personally I leave them off and place images to edge. If you do this use the crop marks and bleed setting when publishing from indesign. Then print on an oversize a4 and crop it down, this should avoid the printer cutting of the edges of your work.
I would also add scalebars to the original drawing, that way you get some sense of the proportionality of the drawing even if its not to scale.
If its a single ‘carry-in copy’ you’re producing it might be worthwhile trying to get a ‘book’ style folio (Pina Zangaro do good ones!) This will allow you to run artwork (particularly sections) across two adjacent pages to keep the the drawing at a large enough scale to still be readable.