Four attacks (+12/+7/+12/+7).
Full Attack: 2 morningstars +12/+7 melee (2d6+6) or 2 javelins +5 ranged (1d8+6)
Whenever a creature in the Monster Manual wields multiple manufactured weapons and its attacks are divided between primary and off-hand, the statblock always makes this clear by stating them separately. Compare it to the three-armed athach (Monster Manual p.21):
Full Attack: Morningstar +12/+7 melee (3d6+8) and 2 morningstars +12 melee (3d6+4) [...]
The athach's first morningstar is primary, so it can make iterative attacks. The other two are off-hand (Multiweapon Fighting, Monster Manual p.304), and stated separately. The same occurs with the marilith (p.44):
Full Attack: Primary longsword +25/+20/+15/+10 melee (2d6+9/19-20) and 5 longswords +25 melee (2d6+4/19-20) [...]
This makes it clear that if the ettin was intended to wield its second morningstar off-hand, it would normally be stated separately, like in the the athach statblock.
In fact, according to Monster Manual p.6, "Full Attack", weapons listed as the first entry in the Full Attack entry are always primary weapons:
This line shows all the physical attacks the creature makes when it uses the full-round action to make a full attack. It gives the number of attacks along with the weapon, attack bonus, and form of attack (melee or ranged). The first entry is for the creature's primary weapon [...]
Both of the ettin's morningstars are therefore primary, meaning that neither of them are off-hand. This means it's not fighting under normal Two-Weapon Fighting rules (which only apply when one weapon is off-hand), and therefore the limit of a single off-hand attack does not apply.