This phrase is often used playfully, to imply a secret understanding between people without stating it outright. She mentioned she loves cooking for 'someone special' lately, nudge nudge, wink wink.
Pro Tip 2/3
Not Literal
'Nudge nudge, wink wink' is not taken literally. It's a metaphorical gesture suggesting you're hinting at something. He spends a lot of late nights 'working', nudge nudge, wink wink.
Pro Tip 3/3
Shared Secrecy
Use this phrase when you and the listener share knowledge of the innuendo or hidden meaning. She said she's good with her hands, nudge nudge, wink wink.