Ok, tried this with my Hotmail account.
There are two ways to insert links.
One is to just type them in, this does not wrap the link in the appropriate HTML markup "<a>", so it just stays plain text, and is not clickable in AquaMail.
The other is to use the "link" icon in the tool bar. This inserts an anchor "<a>" which is then clickable.
I believe Hotmail should scan for and convert all links, but...
...I'll see if I can make the app detect links without an enclosing anchor and highlight them.