File extensions have no bearing on search engine rankings.
What you're seeing is most likely a result of poor coding. But that does not mean that carts programmed in any server-side parsed language are more visible to the search engines than another server-side parsed language. In fact, the engines can't even tell what server-side parsed language you're using: the extension can be falsified!
Two ASP cart owners have just told you that their carts have been successfully spidered with good results.
Now, back on topic:
sun818 is right - time constraints may stop you from rolling your own cart. In that case, you may have to pick an available one which suits your needs. The original poster asked for a recommendation though, and mine is to roll your own (or find a good programmer who can).