It’s best to ask such questions like yours in:
To your question… it depends on the use case. For PvE It’s usually best to use T2 ammo and to setup your ship for maximum DPS in order to run missions and sites as quick as possible. For PvP does it depend on the specific ship and how you intend to use it. There you’ll see both faction and T2 ammo being used. T2 ammo often brings not only benefits but can have drawbacks, too, while faction ammo is often just a better version of the T1 ammo. Hence can faction ammo sometimes be better, because they lack the drawback of a T2 ammo type.
Some examples…
Hybrid Void S:
25% reduced optimal range.
25% reduced tracking speed.
50% reduced falloff range.
15.4 damage.
Hybrid Null S:
40% increased optimal range.
25% reduced tracking speed.
40% increased falloff range.
11 damage.
Caldari Navy Antimatter S:
50% reduced optimal range.
13.8 damage.