Percent was a mathematical term, expressing the number of something as a fraction of one hundred.
In 2267, Earth probe Nomad attacked the USS Enterprise, which caused the deflector shields to absorb energy equivalent to ninety of the ship's photon torpedoes. The energy used for the shields to repulse the attack reduced shielding power twenty percent. According to Spock, they could resist three more such attacks, while a fourth would shatter their shields completely. Nomad later made alterations to the ship wwhich increased engine efficiency fifty seven percent. However, this threatened to destroy the ship as Its structure not stand the stress of that much power. (TOS: "The Changeling")
In 2372, the Ferengi imposed an unfair 6 percent tariff on woolen goods they traded with the Karemma, claiming that the tax was added to help offset the "lost income of Tarkalean sheep herders." (DS9: "Starship Down")
The same year, Seven of Nine was given a list of dietary requirements by The Doctor; "two hundred fifty grams glycoproteins consisting of 53 percent polypeptides and 26 percent fibrous glycogen". (VOY: "The Raven")