It depends on what multi you are using.
If you made one yourself using Windows 10 as a base, then you won't get reboots at random. If you made one using one of the original game Windows installs as a base, then there is a high chance you will get random reboots, the JVS timeout/reboot system (feature) is built into original game images, some but not all.
However.. IF you are using joehowse version of fastio2kb for controls, this has jvs timeout prevention built into it, so this will actually stop the random reboots happening on the Windows image that have it built in. Best way to build a multi is to install yourself Windows 10, the LSTC branch is best, and then just use artfates nesica styled menu to boot at startup.
You can either use fastio2kb for fastio controls, or you can use nikos jvs2kb for jvs controls.