Quartz isn't durable enough for hypersonic IR windows in dense atmosphere. When tested decades ago, actively-cooled sapphire, diamond, and even more durable exotics ablated too quickly for that purpose. I don't know what they are using today but the inability to find an IR transparent material that could survive long enough was a central design problem. This can be seen in the odd compromises made to the seeker design of e.g. THAAD, which doesn't spend much time in the lower atmosphere.