You lose stated stats by equipping non-optimal gear for your class. Like Mickey said, the tests I've seen show about 1/3, so if you have an item that has 30 defense, you'll only be getting 20.
I haven't done or seen any tests as it pertains to your rank vs. optimal rank, but I imagine it's similar to FFXI's level sync'd gear. Basically, your rank 38 item will give you stats that are a little bit worse than the gear that is of proper rank. If you're min/maxing, then you'll want to wear gear as close to your optimal rank as possible, but if you're simply leveling or ranking up, then you'll find that gear that used to be optimal is getting beat out by your better level sync'd gear.
As for your question on using the rank 1 harpoon vs the rank 9; you'll level up fast so even if the rank 1 is better initially the rank 9 will very quickly become the better option. The only downside to the rank 9 will be the extra repairs.
Gear and Weapons that are above optimal level do indeed break faster; so the cost to use them is increased not only by the required repair material being more expensive, but also by the fact that it'll be losing durability faster.