Actually not all legendaries are banned for the Battle Frontier in Emerald. Only Mewtwo, Mew, Ho-oh, Lugia, Celebi, Kyogre, Groudon, Rayquaza, Jirachi and Deoxys-Speed are banned, meaning some legendaries like the legendary birds are permitted.
As for why the previously mentioned Pokemon were banned, it is because they are deemed overpowered. They remove the challenge of the Battle Frontier and make things unfair. Many of them, especially the cover legendaries, are often banned in competitive tournaments, not just by the game.
More info on the Battle Frontier