There are two questions here. Let me address the first one.
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Smartphone malware and Windows
If you have smartphone-malware on your smartphone, it’s not going to impact Windows. Smartphones run a completely different, incompatible operating system than Windows, in the form of Android, iOS or others. Even if the malware could run, it would fail miserably.
On the other hand, what does it mean to have Windows-based malware on a smartphone?
Windows malware on your smartphone
Many smartphones can be connected to your PC and laptop. When they are, your smartphone appears as if it were a USB-connected disk drive. You may have been even treating your smartphone as if it were a thumb drive.
If this is the case, then it might be a different story, particularly if you have an infected file or program.
If Windows malware is on the smartphone, you plug it into your computer, and autorun is running, the Windows-based malware could start running and infect your machine.
If you’re using your smartphone to carry software from one place to another, there’s nothing special about the smartphone that would inoculate you from malware. It’s still going to have the virus. In that sense, the smartphone can certainly still carry viruses.
Protect your smartphone and your machine
All of the usual caveats about staying safe as you use your computer apply in this case. Make sure you’re anti-malware tools are running and up to date. Turn off Autorun and Autoplay if they’re turned on.
It’s pretty much exactly like having a USB thumb drive. Just look at it that way and you’ll see all of the same kinds of risks and rewards from having that kind of technology.
As to your second question, if a USB port is disabled, it can’t be used to transmit anything back or forth, be it malware or good stuff. But it doesn’t inoculate your system. There are still other ways of getting malware onto your system, but disabling a port should prevent that port from being able to be used to transmit malware in either direction.