There were different systems of notation, including some devised since, and parallel to, what we use today. They've just not survived. When I was a kid, someone found an inscription that wasn't in a (known) language, and the researcher involved interpreted it as a musical score, intuited how it may have been notated, and someone performed it.
Music styles change, tastes change. Also, stuff just gets misplaced. Antoine Brumel (15th-16th century, ecclesiastical composer) has a number of surviving works, but the one considered his masterpiece only survived in fragments. In the late 1980s, a very large lost fragment was found between the pages of some old book in Denmark (!) and reunited with the parts that had not been lost. A little remained to be found, but the modern arranger made up something, and the entire work (with the modern bridge) was performed for the first time in perhaps 400 years.
I read about it fifteen years or so ago, had to special order it, and it's easily one of my favorite CDs. There's a new, remastered version of the recording now, plus it has been recorded by at least one other ensemble.