If the box says "Helix 9 Chirp Mega SI+ GPS G3N CHO" it only has the control head and no transducer. "CHO" means control head only. Best to get the actual Humminbird part number and check it against the item on the humminbird website.

Helix 9 CHO = Item # 410860-1CHO <- notice the "CHO" in the part number (Control Head Only, no transducer)
Helix 9 with transducer = Item # 410860-1 <- notice it does not include the "CHO"

My Helix 9 (Item # 410860-1) came with a rubber cover. Pretty sure they are included. You would have to compare the dimensions of the units to see if the cover you bought will fit. All info you seek is on the Humminbird website.