I wouldn't quite describe them as "interchangeable", but the 1.6 swap is a fairly simple & very popular way to get a few more horses under the hood - I've never done it, but as far as I know, it requires an adapter to mate the Samurai bell housing to the Sidekick/Tracker block, along with I think modified engine mounts - you can then swap the fuel injection from the Sidekick/Tracker or go with a carb depending on your personal preferences - swapping the fuel injection is a little more work and can be challenging for those of us who are not handy with wiring.
The reason I mention this is your vehicle may have unique modifications depending on who did the engine swap, so you need to be prepared for some degree of confusion & head scratching - it's not going to be as simple as a 1987 vehicle with a 199x engine - yours could have the Samurai Hitachi carb or the Sidekick/Tracker throttle body injection, maybe a Weber carb, or one from another vehicle - a Holley from a Ford Pinto, or an Aisin from a Toyota Corolla - the combinations are endless - some folks have even used Harley Davidson carbs.
I'm not trying to scare you - the Samurai is a fairly basic vehicle, almost none of the electronics that make newer vehicles challenging - you just need to be prepared to spend some time figuring out what was done and perhaps redoing some of it.