Yes. Caesar describes using several forms of missile warfare from ships at one time. He is invading Britain in the late summer of 55 BCE, and his soldiers are having difficulty getting ashore in the face of stiff opposition from mounted Brits. From Caesar's Gallic Wars book 4, section 25:

*Quod ubi Caesar animadvertit, nāvēs longās, quārum et speciēs erat barbarīs inūsitātior et motus ad usum expedītior, paulum removērī ab onerāriīs nāvibus et rēmīs incitārī et ad latus apertum hostium constituī atque inde fundīs, sagittīs, tormentīs hostēs propellī ac submovērī iussit; quae rēs magnō usuī nostrīs fuit. Nam et nāvium figūrā et rēmōrum mōtū et inusitātō genere tormentōrum permōtī barbarī constitērunt ac paulum modo pedem rettulērunt. *

"When Caesar noticed [the struggles of his soldiers to get ashore], he ordered the longships, the appearance of which was rather unusual to the barbarians and the movement of which was useful in the situation, to be moved away a bit from the cargo vessels and to be urged forward by rowing the oars and to be stationed on the exposed flanks of the enemy, and from there for the enemy to be pushed back and dislodged from their position by means of slingstones, arrows, and tormenta bolts; this idea was greatly useful to our soldiers. For the barbarians, thoroughly frightened by both the sight of the ships and the motion of the oars and their inexperience with [tormenta bolts], stopped short and moved back a bit."

I cannot recall any visual media that shows missile weapons on roman longships. The tormentum was not very big, though too big to be hauled around by one soldier. It was typically mounted on a stand. I don't recall any mention of larger projectile weapons on warships, however. The longships were fairly sleek and narrow.