You can add something like
<?php echo number_format($this->item->extraFields->extrafield-alias->value); ?>
for your extrafield, if you want just one to have this replace the line
<span class="catItemExtraFieldsValue"><?php echo $extraField->value; ?></span>
to this
<span class="catItemExtraFieldsValue"><?php echo number_format($extraField->value); ?></span>
in both category_item.php and item.php files in the foreach element.
Note that your code will break if you put anything but a number in the values of your extra fields.
Also, if you are not using template overrides you need to. Read here
getk2.org/documentation/tutorials/174-templating-with-k2-and-the-concepts-of-sub-templates how template overrides for K2 work.