If we have a character who is supposed to be a skilled crafter, such as a smith or a carpenter or a mason, should we, for roleplaying purposes, put ranks into any or all of the three crafting skills? When I mean roleplaying purposes, I am refering to times such as when DMs ask you to make a persuade roll or a heal roll in events or in plots.

Also, if we take ranks in these skills, will they end up being applicable in the new crafting system that is yet to come? Or will that system not use Bioware skills?

The new crafting system won't use Bioware skills -- it will really be pretty bare-bones.

"Craft Trap" will be used in Engineering-type rolls (for example, for setting up and operating siege equipment).

I don't think we've really decided on what Craft Armor and Craft Weapon will do, or how they will be used. My herbalism/ritual/alchemy system isn't going to use them, as far as I know.