Whenever talking to Kapp'n, in regards of going to the the island, he always says, 'Most of your stuff will be here when you return' not ALL of your stuff :/ So, does this mean that if certain items are in your inventory, he'll take them?
no, all that happens is that your inventory before going to the island is kept safe and you get a full new inventory on the island . once your at the island and get items there (bugs or furniture ) you store them in a box. once you return your original inventory is back.
note if you have any items in your inventory when return to your village then they will be lost
Nope, as already stated he will give you all of your items back when you return home from your island. He does this so that you have full inventory to catch things at the island.
Once you get back it all your stuff you had before leaving will be in your inventory as normal.
No. Once you leave your town then come back all of your stuff will be in your inventory (including bugs, fish etc.). However at the island if you forget to put some things you have collected in the box then they will be sold for a tiny amount of bells.