You should always link to your canonical URLs for SEO. There is no reason to expose your URLs with
index.aspx on them.
- They are ugly
- They are longer
- You would prefer the other version gets indexed by search engines.
Duplicate URLs like this rarely confuse search engines that much anymore. When Google finds duplicate pages, it ignores one and chooses one to index. When you use canonical tags, it usually chooses your canonical to index. See What is duplicate content and how can I avoid being penalized for it on my site?.
The biggest problem with linking to non-canonical URLs is that is a signal to Google that maybe you actually prefer that version. In some cases, Google will choose to index ugly URLs rather than canonical URLs when it finds other signals such as links, or inclusion in the sitemap that indicate they may be important.