Conflicts between plugins are up to individual developers to avoid. As much as possible, anyway. That's a downside of a large open community like this, there is no guarantee that different plugins are compatible or even tested in combination.
So yes, keeping the number of plugins limited will help :) ... Of course, it will also keep site speed at a decent level as some plugins tend to eat a lot of resources. While others are designed to improve site performance.
I can imagine it seems like a dense forest but since you are already quite active on these forums, you will probably have some clues about how to spot valuable and well kept plugins and how to avoid the lesser ones ;)
In any case, another important factor in reducing conflicts is the theme. Thanks to not deleting the link I could take another peek ( ;) ) and beside the fact that it looks fantastic, there are some improvements that can be made: there seem to be many script files (starting with jquery.min.js) included by 'hard code' in the footer.php template. This is asking for conflicts because this way, WordPress has no way of knowing what scripts have been loaded already and so no way to prevent doppelgängers.
Basically, what needs to be done is remove these hard-coded lines and move the inclusion of scripts to functions.php, using
wp_enqueue_script. Start with reading http://codex.wordpress.org/Function_Reference/wp_enqueue_script (you can find some great tutorials in the Resources list at the bottom too)
Note that it is the
$handle that WordPress uses to detect double inclusions so be careful in choosing the correct handle name. There is a list on that same Codex page of scripts that come with WordPress with their correct handle name. Other scripts you'll have to name yourself but here are some tips:
jquery.mousewheel.js should use the handle 'jquery-mousewheel' (use hyphens)
jquery.jscrollpane.min.js should use the handle 'jquery-jscrollpane' (ignore min)
Good luck :)