Someone would have said it earlier, but the bombs are planted in the last tape. He would have noticed the "V" too.
As for Paz/Chico in the cage... I think this is definitely alluding to her not really knowing how to relate to people. She puts on an act, but her "true self" is really something very twisted (not that she is intentionally trying to be squicky). It's clear Zero shaped her in a very specific way to follow his orders, and that could have left her emotionally tone deaf or something.
One thing that's important to note is that both Paz and Chico were effectively raped. Paz was clearly the focus, but it was also a violation of Chico, he was being tortured too. That's something that it seems the IGN writer ignored.
Edit: Yeah, when I first discovered the Chico/Paz rape thing I was like "Eugh!", but when I learned about the part after it added another layer of "do not want" to the situation. Basically, Paz be crazy, but it's a situation where everything was out of control. Trying to initiate "contact" was probably her way of trying to cope with the loss of control. For her, she was trying to help Chico deal with the trauma (in pretty much the worst way possible), but also she was trying to help herself deal with loss of her control of her own self and body. Disgusting, but if you look at is a symptom of deeply rooted control issues (hello, Cipher training) it at least makes a twisted kind of sense.
Edit 2: I'm surprised I haven't heard anyone mention the little piece of information Kaz gives Big Boss about Amanda's reaction to Chico's rash actions. It happens when you sneak around the holding cell area past the roof that sometimes has a car under it. Kaz informs Big Boss that Amanda told him to tell Big Boss she was "ready for the worst" and remarks that she sounded "a little too cheerful to me". Creepy. Was Amanda subtly giving her consent to "silence" Chico? After all, in Peace Walker she asked him to kill Chico if he sold out his comrades. More juicy potential future things to happen to Chico in TPP, if he makes it through BB's coma, Kojima truly is god.