our son does this too, for no reason in particular. sometimes hes in our bed, sometimes hes on the floor.
i have found that the best way to deal with it is to not "deal" with it. obviously he has a need, and in my parenting i have found it best to let him outgrow the need instead of making him. after all, if hes ok with sleeping on his own place on the floor, whats wrong with that? i dont think theres anything wrong with that at all. i doubt you have any worries about intimacy unless you are one of those couples who makes time at 1 am for that! :P
but you have to remember, above all, that YOU are his parent, so what YOU feel is best for your family and your son is what is important. you probably know inside what is best, and even if it goes against "popular advice or wisdom" you need to follow what you know is best for you.