For two reasons, I believe Bond did not sleep with Eve Moneypenny.
First, the Bond series usually makes it clear when James has sex with a woman. There are very few love scenes that are ambiguous -- but the scene with Eve is ambiguous.
Second, Skyfall introduces Moneypenny, but I don't think Skyfall changes the nature of her relationship with Bond -- and in all the preceding Bond movies that feature Bond and Moneypenny, their banter suggests he wants sex but she insists on commitment first. Moneypenny often mentions things like engagement rings, while Bond makes loads of sexual references. Also, their flirting consistently strikes me as having a hopeful tone suggestive of the tension of a relationship yet to be consummated -- not the more knowing tone suggestive of a prior, brief sexual relationship:
Dr. No (1962)
- Moneypenny: 007 is here sir.
[Slaps Bond's hand away from the papers on her desk]
- Bond: Moneypenny! What gives?
- Moneypenny: Me, given an ounce of encouragement. You've never taken me to dinner looking like this. You've never taken me to dinner...
- Bond: I would, you know. Only "M" would have me court-martialed for... illegal use of government property.
- Moneypenny: Flattery will get you nowhere - but don't stop trying.
- Bond: What do you know about gold, Moneypenny?
- Moneypenny: Oh, the only gold I know about is the kind you wear... you know, on the third finger of your left hand?
- Bond: Well, one of these days we really must look into that.
- Moneypenny: How about tonight? You'll come over for dinner...
[playfully tosses Bond's hat onto the hat rack] and I'll cook you a wonderful angel cake.
- Bond: Well, nothing would give me greater pleasure, but I'm afraid I have a... business appointment.
- Moneypenny: [laughing] That's the flimsiest excuse you've ever given me. Oh, well, some girls have all the luck. Who is she, James?
- M: [over intercom] "She" is me, Miss Moneypenny. And kindly omit the customary byplay with 007. He's dining with me and I don't want him to be late.
- Moneypenny: [to Bond] Then there's hope for me yet.
- Bond: [gives Moneypenny a playful peck on the cheek] Moneypenny, won't you ever believe me?
You Only Live Twice (1967)
- M: [buzzing intercom] Miss Moneypenny, give 007 the password we've agreed with Japanese S.I.S.
- MoneyPenny: Yes sir. [to Bond] We tried to think of something that you wouldn't forget.
- Bond: Yes?
- MoneyPenny: "I, love, you". Repeat it please, to make sure you get it
- Bond: Don't worry, I get it.
Diamonds Are Forever (1971)
- Bond: What can I bring you back from Holland?
- Moneypenny: A diamond? In a ring?
- Bond: Would you settle for a tulip?
- Moneypenny: [Bond leaves; she sighs longingly] Mm, yes.
- Bond: What would I ever do without you?
- Moneypenny: As far as I can remember, James, you've never had me.
- Bond: Hope springs eternal.
- Moneypenny: You know, this sort of behaviour could qualify as sexual harassment.
- Bond: Really? What's the penalty for that?
- Moneypenny: Someday, you'll have to make good on your innuendos.
- Bond: After you, Moneypenny.
- Moneypenny: No, I insist. You first.
Tomorrow Never Dies (1997)
- Bond: I doubt if she'll remember me.
- M: Remind her. Then pump her for information.
- Moneypenny: You'll just have to decide how much pumping is needed, James.
- Bond: If only that were true of you and I, Moneypenny.
The World Is Not Enough (1999)
- Moneypenny: James! Have you brought me a souvenir from your trip? Chocolates? An engagement ring?
- Bond: I thought you might enjoy one of these. [gives Ms. Moneypenny a cigar tube]
- Moneypenny: How romantic. I know exactly where to put that. [throws the cigar tube in the garbage]
- Bond: Oh Moneypenny, the story of our relationship: close, but no cigar.