Even with a few maxed out Bunkers, which I could afford at the time, I couldn't destroy the boss enemies. I almost destroyed a second boss. The regular enemies are easy to destroy, compared to the bosses. The bosses seem to be too strong.
The best way to deal with the ninjas is to place the towers near the entrance to the battlefield and to place them near the cave where the gems are. The smoke bombs can't last forever. The ninjas are vulnerable to the rapid-fire upgrades of the towers. A good kill box near the gems can finish them off. You might have to add many towers because other enemies can distract the towers.
I think that Arcuz: Behind the Dark is shorter version of Arcuz (full game). I'm not sure which chapter the game stops. You definitely can't beat Arcuz: Behind the Dark.
Glad you like the game. What game?