Definitely put the conduit in.
Both LV landscape wires and sprinkler wires are subject to damage. Once they have been damaged and spliced, they are subject to water intrusion and corrosion if the repair splices are not perfect. Over time, you may not have any recourse other than replacing the wires under the patio.
Do you want to tear up the patio at that point ?
The only other good solution is to look for another location for the LV transformer and sprinkler control. You could relocate them now and avoid wires under the patio.