The main issue is not just protection; it’s the optical path length to the sensor.

In an IR conversion, simply removing the original filter can change the sensor stack thickness. That affects where the image comes to focus. For phase-detect autofocus, this is especially important because IR light focuses at a different point than visible light, so an unmodified PDAF system will usually be off. A properly chosen replacement glass can shift the effective sensor position so autofocus is calibrated for IR.

So yes: cameras using phase-detect AF generally need more than “just empty space” where the filter was. They typically need a replacement with the right optical thickness, or AF accuracy will suffer.

Contrast-detect AF is less dependent on factory AF calibration because it focuses from the sensor image itself, so it is generally more tolerant of changes in the sensor stack.

As for leaving the sensor uncovered: even if the camera body is closed, removing the protective glass layer leaves the sensor more exposed and is generally not ideal. In practice, replacement glass or a dedicated IR-pass filter is commonly used both to maintain the optical path and to provide protection.