A federal magistrate in Baltimore threw out yesterday a jury's award of over $1 million in damages to hundreds of inmates and former inmates at the Worcester County jail on Maryland's Eastern Shore. The jury made the award last month in a suit contending that the jail was overcrowded and insanitary.

The magistrate, Frederic N. Smalkin, said he was vacating the award, even though the jail may have been overcrowded, because the amount seemed only punitive, while not compensating for any real injury suffered by any inmates.

"There was no medical evidence," Smalkin wrote in his long decision, "that any identifiable member of the plaintiff class the prisoners suffered permanent or even transitory post-incarceration mental or bodily disease attributable to the jail."

The jury's verdict, unprecedented because of its size and the hundreds of persons thought to be affected, would have awarded $500 to each person being held in the jail awaiting trial between July 19, 1977, the date the suit was filed, and Oct. 1, when the jury reached its verdict. Convicted prisoners being held during that same period were eligible for $1,000 each.

County officials had estimated that at least 1,400 persons were eligible for the payments, which would have severely drained the county government's coffers.

The suit had charged that the jail at Snow Hill was overcowded and at times insanitary because of leaky plumbing and structural problems. Some toilets did not work, and prisoners without beds who were forced to sleep on the floor complained of being splashed with urine during the night.

The jail has 57 beds in dormitory-type cells with six, or sometimes nine, inmates in a single cell. The most prisoners ever held there was 80 at one time during the summer of 1980, Yankus said, and some were forced to sleep on the floor on matresses.

The county is building a new, $4.7 million jail, scheduled for completion next year, which will house about 100 prisoners, each in a separate cell.

Smalkin said that if his decision if overturned on appeal, the county is at least entitled to a new trial.