Não há limite para o número de variáveis AFAIK, mas existem alguns limites para seu tamanho (dependendo da versão do sistema):
The maximum size of a user-defined environment variable is 32,767 characters. There is no technical limitation on the size of the environment block. However, there are practical limits depending on the mechanism used to access the block. For example, a batch file cannot set a variable that is longer than the maximum command line length.
Windows Server 2003 and Windows XP: The maximum size of the environment block for the process is 32,767 characters. Starting with Windows Vista and Windows Server 2008, there is no technical limitation on the size of the environment block.
n.b. o comprimento da linha de comando que eles mencionam é 8191 caracteres.