I never use hyperlinks in books. 90% of the books in my library are ones I compiled myself from HTML or Rich txt documents. I tend to go in and remove unwanted items like Table of Contents (lots of links there) as well as junk like page after page of copyright, samples of other books, etc.
I used to have VERY strict guidelines for any book that ended up in my library. I would recompile with the book cover as the first page, a smaller book cover as the actual cover (shows up on the bookshelf) and following the std format where the file name is AUthor last , author first - series number - title (example: Rowling, JK - Harry Potter 01 - Harry Potter and the Sorcerers Stone)
Up until about 5 months ago, MOST books started out as HTML and then converted to a MS WORD doc( this lets me get the format just right), then converted to a MOBI via Mobipocket creator (so I could add the author and book cover correctly via meta data) then converted into an epub via Calibre. Recently I got a little lazy, and just get the epub directly and use Calibre to modify the metadata if need be. This does give me some small formatting errors, but its livable.
In your case, Aldiko does have Margin settings. You can adjust the size of the margin, as well as set it to justify LEFT, RIGHT, or CENTER.
Not sure what can be done about the hyperlink issues.
Aldiko also offers you the ability to set up a "shortcut" via widgets directly to a specific book on the homescreen.