Are 2B's and 9S's default swords the same?

Aside from lore and appearance for Virtuous Contract and Cruel Oath, the main difference is the unique ability the weapons receive at lv4

Virtuous Contract receives the Holy Blessing ability where as Cruel Oath receives the Dark Impulse ability

Weapon Effects

Holy Blessing Increases attack power when HP is full.

Dark Impulse Increases attack power when HP is at 30% or less.

As a side note, attack does contain a slight difference at lv3 with different power for heavy

Virtuous Contract

lv3 - Attack: 420 - 504; Light: 6; Heavy: 3

Cruel Oath

lv3 - Attack: 420 - 518; Light: 6; Heavy: 2

Looking at the Wiki pages for both of these swords shows that the only difference between them is the materials needed to upgrade them.

• Cruel Oath
• Virtuous Contract

The one exception appears to be at level four, where the Cruel Oath gets the Dark Impulse effect, and Virtuous Contract gets the Holy Blessing effect. Dark Impulse increase attack power when under 30% HP, while Holy Blessing increases attack power at full HP.

As noted in the other answer, at level three for Virtuous Contract, the Heavy combo is +1 higher than Cruel Oath, and the Attack Value has a higher maximum at 518.