I'm using SearchEngine contraption, I'm not sure if I can "override" the links displayed in this prototype?
You'd need to modify the contraption prototype, but it's a very simple change. In the SearchEngine the results are displayed in a rich-text field named "o". It doesn't currently contain any scripts and simply relies upon the default "on link" behavior.
The main thing to be aware of is that within a Contraption you won't auto-magically have cards and widgets of the deck in scope as variables; You do have access to "deck", though, so you can use fully-qualified paths to reach out to a specific widget. e.g. "deck.cards.theSearchCard.widgets.theSearchCounter", and if you use go[] you can refer to cards by name (as strings) instead of value (as cards).
I've tried to make all the contraptions in the bazaar as generic and reusable as possible, but don't be afraid of hacking them up or making changes to suit a specific application. In the worst case you can always delete the prototype and re-import the reference copy.