Technically silicone vacuum lines (black) are not illegal when used specifically to replace existing vacuum lines; at least we haven't found any documentation saying they are legal in California, but nor have we found anything that says they aren't legal. We know mixing and matching is not allowed; you can't use a silicone vacuum line for a fuel line, or for any part of the PCV system... common sense dictates this, and it will be considered an emissions tamper. But replacing a standard vacuum hose with a silicone hose, should not pose a smog check problem, let alone cause your car to fail the smog check.
Since the implementation of the STAR smog check program, smog technicians are very cautious on passing vehicles which might appear to have a tamper. Playing it safe, they'd rather fail the vehicle.
We'd recommend contacting the Bureau of Automotive Repairs (800) 952-5210 and speaking with a BAR inspector for final word. Once you've got their name, and their acknowledgment that black silicone rubber vacuum lines should not cause a smog check failure, take this information back to the smog station which failed your vehicle and ask them to retest it. This is the best option in this case. Unless the BAR inspector says otherwise, your car should not fail for having silicone vacuum line(s). If the BAR inspector says the silicone lines are illegal... then your stuck. Replace the vacuum lines and get another retest. We believe you will get the same information from the BAR inspector that we've mentioned here.