Hello,
I agree virtual probes save costs but there is other risks as highlighted, you can in theory convert the software on the probe to a VM however it would likely involve dismantling the probe and I'm pretty sure RIPE Atlas would be happy. For each virtual probe you would need a physical so pretty pointless.
Luckily they don't use a lot of power or space and easily fit in racks, cupboards or even down the back of your sofa depending on where your router is.
Anyway hope this helps.
Regards,
Tom