What does the “S” above the ICXC mean?

It’s not an S, per se; you’ll usually see it as just a bar, or a semicircle. Zeibura S. Kathau unearthed an instance that looked like a capital omega. It’s an abbreviation marker: Ι͞Ϲ Χ͞Ϲ is an abbreviation of IHϹΟΥΣ ΧΡΙϹΤΟϹ. The convention is particularly prevalent for Nomina sacra, divine names and titles.

Here’s Wikipedia’s illustration from the Codex Vaticanus of the Bible (4th century), with Ι͞Υ (IHϹΟΥ = of Jesus) and Θ͞Υ (ΘΕΟΥ = of God):