This isn't really a good idea. We fix hundreds of these a week because SVG title/cover pages will not display correctly on Kindle devices 1 - 3
I assume you mean they don't convert
well to the Kindle format... since ePubs are mostly worthless on a Kindle anyway.
Your point is taken, of course, but you can hardly condemn this fairly standard ePub practice without making the assumption that every single ePub is also a mobi source document.
So yes, if making a single (easily maintained) source document to use for ePub and MOBI is high on your list of priorities, then it's best to not use the SVG wrapper. Otherwise... there's absolutely no reason not to use it in an ePub.