It depends how you're swapping it. One way to reduce memory pressure is to dynamically insert different iframe
src values into a single frame. So you would place a rectangle, give it an ID of 'scene1box' and then use this code to dynamically insert the iframe code you wish:
var soundcloud1 = '<iframe src ="https://w.soundcloud.com/player/?url=https%3A//api.soundcloud.com/tracks/313222609&auto_play=false&hide_related=false&show_comments=false&show_user=false&show_reposts=false&visual=true&sharing=false" width="100px" height="100px" scrolling="no"></iframe>';
document.getElementById("scene1box").innerHTML = soundcloud1
You could do this with Hype documents, youtube embed codes, or whatever you wish. But I think you should test out the performance of your document with several iframed elements at once and see how it performs -- it may be completely fine. If you load 5 youtube embeds, a lot of the code for those will be reused across the videos so it's not as huge a memory impact as you may think. Loading multiple Hype document within a Hype document might slow things down, depending what you've got in there.
Setting elements to 'Display: Hidden' in the Element inspector while your elements are off scene will alleviate some graphics memory needs (this will be most noticeable on mobile). But the elements will still be loaded into regular memory if you are on the element's scene.