If the pipes are in the walls, I see no reason why you couldn't use a permanent cap for the vents. As for the shower and toilet, when I have folks that want to remove plumbing in a slab I'll have them "dynamite" it. Wad up some newspaper and shove it down the drain, make sure it's snug and that you've pushed the newpaper wad at least 3-4" down into the pipe, fill with grout and smooth over. You can do the same for the vents if you find you don't want any piping sticking up out of the floor. Easy as pie!