The USNS Sacagawea (the second in the line of Lewis and Clark class ships) is armed with 2 to 6 12.7 mm or 7.62 machine guns.
Don’t see any armament listed for the USNS Lewis and Clark.
Correcting a design flaw maybe with the Sacagawea?
Very small military contingent - guns require maintenance - that means Gunners Mates and that means more military crew and that means more expense. The whole point of the USNS fleet is to provide logistical support to the combat fleet at a lesser cost than using regular Navy ships. Also, the USS fleet is limited in their deployment lengths - the USNS fleet has fewer restrictions on op-tempo.
Still that doesn't explain why one of our vessels can be pursued for an hour without some sort of response from a combat vessel or from the air.