> Doesn’t silent, invisible, intangible also apply to software?

No. Because software is hardware.

> You can’t really tell a particular piece of hardware is running software by a direct physical measurement. You can only infer that indirectly.

You can literally step through code. Have you ever used a debugger or a profiler? You can dump memory, check the registers, read off the disk, etc.

If software was silent, invisible and intangible, you couldn't store it on disk, or copy it to memory. A computer wouldn't work if software was as you describe it.