Yes, the current version of Grapher opens graphs created in previous Grapher versions (Grapher 2 and all newer versions). We try very hard to maintain compatibility with files created in older versions. If you have an older GRF file that does not open in the current version of Grapher, you can follow the instructions here to convert the file to a newer format.
After opening an older file in a newer version and making changes, you can save back to an older file format by following the instructions here.
Updated January 12, 2018