Compared to the Ninja Trooper, who is available much earlier and is actually the predecessor, the Shinobi actually pales in comparison in many ways. While most stats remain the same, the Shinobi does less damage and has less HP. Also, the Shinobi is available at player level 65, and costs a lot more resources to promote when compared to the Ninja Trooper. These differences mark the advantage of spending Nanopods on the Ninja Trooper.
Regardless, the Shinobi is still an effective unit to utilize and does not cost Nanopods. A Rank 2 Shinobi matches the power of a Rank 1 Ninja Trooper.
Note that the Ninja Trooper gets its third ability slot at Rank 3 while the Shinobi gets it at Rank 4.