Clear creatures

I am confused about how some creatures can be clear, or at least mostly clear. One example is the clear squid (more commonly called the glass squid). How can their organs be clear, their stomachs must produce acid which I assume has some coloring. Surely their blood must not be clear, or is it? And most puzzling to me, how can they produce black inc when they appear clear? I thought that maybe they combined two clear chemicals to produce one black chemical but I wasn't quite sure. Perhapse this just stems from my misunderstanding of how squid work. Thank you in advance for all replies and your assistance to help me further understand this topic.