Fair enough. As I said; my change is more of a "stickler for details" thing.
But if you're cleaning up the cruft from retail epubs, you're going to start running into the <aside> tag sooner rather than later. Both Kobo and B&N (and even Kindle) books are exhibiting more and more html5/epub3 features.
Deleting the <aside></aside> tags and leaving their contents intact could make for some very confusing reading (footnotes and other ancillary details stuffed into the middle of sentences and the like).