Chesters,
The problem with print outs is the price of the ink, which is a rip off no-matter which printer you are using.
Scotlands People is a site I have already spent mountains of money on hundreds of images, so to also have printouts of every single cert would be far too much expense. However, I know that Scotlands People store everything I have bought from them, which I can look it up for free anyway. And I also have the certs on the timeline of the persons concerned. Like yourself, I have the certificates (some of the most important ones)in clear pockets.
I use separate, large art pads to store my mother & father's ancestry, going back hundreds of years. To gain space, I use the old system of placing a tiny number next to the name of any person whose expanded lineage has had to be continued to a different page. Neatness is the keyword. If it isn't done neatly, it won't work, because it won't look good.
I find that visitors are much more at ease looking at these art pads than being taken to my computer, with me standing behind them like a back seat driver giving them instructions how to find things.