I disagree, as an app developer. It would have been easy to include an 'embed hyperlink' option on the formatting popup.
I discovered that you can indeed include hidden hyperlinks in Apple Mail generated on the iPad. You just cannot create them there.
After some experimentation, I discovered that you can paste in text with embedded hyperlink, and it will send and function properly.
The trick is how to create it on the iPad. Even the Pages app won't do it on the iPad. I wish Apple had not chosen to omit this useful feature, as it goes against the idea that you can freely work on the desktop and then on your iPad and vice-versa. Perhaps iOS8 and Yosemite will fix this.
Here is one work-around.
Get an iPad HTML editor such as the free Good Docs. Go into HTML mode (via <> button).
Paste in this code:
<a href="http://indigo.malinowski.com/SHAboutAuthors.htm" target="_blank">Mel Malinowski</a>
Change the link to the one you want, as well as the display text.
Go back to normal view via 'done'
Select the text and copy.
Now you can paste this embedded hyperlink into your email. Great for long, ugly, awkward YouTube links and such.
Awkward, I admit, but sometimes very useful. Hopefully, someday Apple will make this easy and Mac-like. Perhaps someone can post an easier workaround.