Not to get too much into semantics, but if Samon was locked in a crate, his natural rights deprived, he is a de facto slave, whether someone has bought him or not.
As for Profession vs. Craft, you use the Profession skill to earn money and to practice a trade, you use the Craft skill to create things, especially in the sense of items with a listed value in the PH. On an island with no herbal shops or apothecaries, having both a Craft and Profession skill might be necessary in that case. Profession to determine which native species and minerals can be used as spell components, and Craft to make them into a spell component pouch. Arcana, Religion, or Nature could substitute for Profession as specific for their realms of spellcasting (Arcana for arcane spells, Religion for divine spells, Nature for druid/ranger spells).
A spell component pouch is an abstraction created for 3e so that spellcasters would not generally need to track whether or not they had the spell components for the spells they were casting. It would be assumed that the spellcaster was gathering spells as he went along to replenish the mundane spell components he was using. You will need to actually track spell components for the early part of this campaign if you are a spellcaster. If you are a divine caster, you will most likely have to fashion a crude divine focus from wood you find before you can cast spells requiring a divine focus.
I would not worry too much about all of this though. It will be rough going in the beginning. But things will grow easier over time. I don't want to spill all the details so I will leave it at that.
Edit: Bear in mind that your characters did not board the ship INTENDING to get shipwrecked. So you would have had all the things a normal adventurer would carry. Shipwrecks are fairly uncommon in 998 YK. Elemental galleons, expert navigation of Lyrandar ship captains guided by magic, and other things make seafaring much safer than it was during Earth's age of exploration. Also, traveling between Xen'Drik and Khorvaire is more like crossing the Gulf of Mexico or the North Sea than it is crossing the Pacific or the Atlantic, so there is much less danger of turbulent waters and the like. This shipwreck is caused by something... special.