Like PPQ_Purple said, there's a big difference in equipment. Hatamoto Gunners/archers usually get stronger teppo/bows and katanas, and armour. They also usually have Kozane armour that's around 50+ armour. Skirmishers on the other hand usually only get Wakizashi and Retainer level armours in the 35+ range. Ranged samurai really prove their worth when the enemy line finally closes and things devolve into a messy brawl. Skirmishers tend to die very quickly in hand-to-hand combat - their wakizashis have very short reach and generally don't do enough damage to let them kill an enemy before they are shanked.
Secondly, it's likely what you are seeing is the way Warband randomizes stats. At the beginning of every new game, the engine randomizes all NPC stats a little, adding several points based on their level to the default stats that are set for them in the troops.txt. This makes every game a little unique. Thus you'll notice each faction's troops, despite being of identical tier, level, and starting stats, will have slightly different final attributes.
It's possible that the Shimazu gunner in your game got a poor stat spread compared to the Ryujozi Skirmisher you're comparing with. Try comparing several different Hatamotos/Skirmishers from different factions and you'll notice there's some variation in their attributes and HP.
