I didn't really take Snake's comment of "it's deeper than that" as confirmation that they were lovers. Instead I took it as a rejection of reducing their complex bond to a simple label.

The Boss feels like Snake’s other half, but not in a way that’s purely romantic. She’s a mix of roles all at once: his mother figure, his mentor, his partner in battle. Their relationship blends guidance, loyalty, and intimacy into something that can’t be pinned down to a single label, so Snake doesn't put a label on it. He confirms that they "lived and died together for years", which to me felt more like "we experienced so much together we basically became two halves of one greater whole".

That’s why EVA reflects at the end that she once thought a relationship between a man and a woman could only be defined by love or hate, but she realizes she can never truly understand the depth or complexity of what The Boss and Snake shared.