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From the description, you are sideloading epub and the footnotes are "cute" little superscript numbers you can barely see, let alone tap.
If I'm correct, the problem is that the epub renderer is a bit literal in the size of the tap area for the link. If the link is a single character, then the tap area is the area occupied by the single character. If you increase the font size, you will find you can tap the link a lot easier.
The better solution is to convert the book to a kepub. For books with lots of footnotes, kepubs have two big advantages. Firstly, the tap area for the link is much bigger. It is normally big enough that you won't have a problem tapping a small superscript number as a link. The other advantage is that a popup is used to display the note. Or at least the start of the note. If the note is to large to be displayed, you can tap a button on the popup to go to the full note.
The best way to get the book onto the device as a kepub is using calibre and either the KoboTouchExtended driver or the Kepub Output plugin. The former will modify the book during the send to device. With the latter, you convert the book to kepub and then send this.
If you are not a calibre user, there is a tool discussed here recently to convert an epub to kepub and you manually sideload this to the device.
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