The D.C. Board of Labor Relations declared yesterday that the city school system engaged in "serious unfair labor practices" by failing to negotiate with an employee union before deciding to drop 104 employes from the payroll.

The board told School Superintendent Vincent E. Reed to sign and display a nitice promising union members that such practices will not be repeated.

Although the damage was later repaired by putting 99 of the affected employes into other jobs, the labor board said its directive to Reed served notice that public agencies should not "play hide-and-seek" in their dealings with unions.

The long-range implications of yesterday's decision were even more significant. The D.C. City Council recently enacted legislation creating a new personnel system for the city broadening the future role of unions in negotiating wages and contract terms for municipal workers.The decision should strengthen their hand.

The Board of Labor Relations referees labor-management disputes involving funicipal agencies and their employes.

The 104 employes whose proposed layoffs led to yesterday's decision had been hired by the school system as tutorial aides and clerks for a federally financed program to improve reading and mathdematical skills among pupils in Anacostia. The end of funding led to a decision in 1977 to drop the employes.

Before that decision was reached, however, the employes had voted to be represented by Local 2921 of the American Federation of State, County and Municpal Employees, which insisted -- successfully in the end -- that the terms of their termination should have been negotiated.

Because of the holidays, school officials could not be reached for comment.

Yesterday's decision was the second this week in which the labor board decided that educational employes hired for federally financed programs have rights to be considered for jobs on the regular city payroll. In the earlier case, the board ordered the University of the District of Columbia to assign a professor terminated from a special program to a regular classroom post.