The combination of shellholes and orchard can exist in the same hex.
The orchard can also burn:
Further on Orchards:
14.5 An orchard may be kindled on a DR ≥ 11 and Fire will spread to it from an adjacent Blaze on a DR ≥ 9 (both subject to modification; see Section 25).
But nothing is mentioned about them being able to be rubbled or cleared.
If this was a CG then:
CG7 TERRAIN CHANGES: During the course of the same CG, alterations of printed mapsheet terrain are bound to occur, all of which become "permanent" (barring subsequent Clearance/Removal or Deactivation [11.6123] if applicable). All counters for Fortifications, Rubble, Breaches, Trailbreaks, Shellholes and wrecks are left on-map from scenario to scenario. Any terrain Ablaze at scenario end is resolved as per RePh 11.609. A wreck in a terrain Blaze is not removed from play; instead, it remains on-map (still treated as a LOS Hindrance) and in step 11.6091 of the next RePh will become a Burnt-Out-Wreck. 14 A Burnt-Out-Wreck may neither catch Fire nor be Scrounged, nor may it be removed from play as per D10.4. A Burnt-Out-Wreck is a LOS Hindrance in the same manner as a normal wreck.
and
11.6092 BRUSH, ORCHARD, WOODEN RUBBLE: Place a Shellhole counter in the Location; the other previous terrain no longer exists.
would apply. But this is not the case here.