1) Normal "Cell" hyperlinks, handled with Get/SetHyperllink
2)"Formula" hyperlinks, like for example if you write in a cell "=HYPERLINK("http://www.tmssoftware.com")" Those hyperlinks are "old style" from really old Excel versions but they still work today, and if you need to handle them, you need to look at the formulas as they won't appear in the Hyperlink count.
3)Hyperlinks over images or objects. Again, this won't shown in the Hyperlink count properties, as they are a different thing. Those hyperlinks are attached to the objects, and to find them, you need to look at the objects themselves. Note that FlexCel handles image hyperlinks when exporting to html/pdf too, if you export a file with those, you will see the image hyperlinks are exported.
a code snippet you could use to fine the image hyperlinks in a sheet is like this: