Plenty of items and treasure-hunts await Samus aboard the Bottle Ship. How the myriad of items she'll find actually got to their hiding spots is anyone's guess, but each is worth searching for to help increase Samus' chances of survival.
Each Metroid game has a reason for Samus not setting out with all her staple abilities from the opening sequence - this episode is no different. Almost all her abilities discovered on Zebes during the events of Super Metroid are present, but Samus will be co-operating with the Galactic Federation on this mission. More specifically, she'll be following orders from Adam Malkovich, and this includes restrictions on the use of her powers.
During the game, Samus will slowly receive authorisation to use her abilities as the situation calls for their deployment. It's not the ideal working scenario for a bounty hunter, but her respect for Adam and the nature of the mission calls for her compliance with the Federation (and grants Team Ninja an excuse to give Samus a clean starting slate).
Notes: Expansion items (Missile Tanks, Energy Tanks, Energy Parts, Accel Charges and E-Recovery Tanks) will not be present in Hard mode.
Clearing out all enemy targets in a single area will reveal hidden item locations on your mini-map and the sub-screen's map. Finally, upon completing the game (only on Normal mode), all remaining item locations will be revealed as blue glowing dots on your map.