Honestly, I don't think so. She really confided to Daphne as she would have to a friend during that massage session if she suspected anything she would have confronted Niles head on and given him hell as she did before. I think Mel was condescending to Daphne and considered her to be a member of an inferior class of people and at the same time during that massage she tried to be as amicable "to the help" as she knew how, the same way the butler did, although with more diplomacy on his part. During the X-mas episode she practically broke up with Niles twice even though both times she had only a vague suspicion on a blurted word of Frasier (who was quite the blunderbuss then...
)
She's not one to fake affection or to bottle up her resentment. If she suspected anything, even half of a thing, she would have made Niles life miserable until everything was explained to the last detail.
So, in conclusion, my opinion is no, no suspicion whatsoever until the moment when Niles told her and she burst into hysterics.
Besides when Niles and Daphne were in that hotel room with all the people passing by (including Mel and Donny) . The only people who realized that something was going on were Martin and her brother Simon (who for all his flaws is quite perceptive).
Frasier: You started us down that path of insanity. Golda Meir.
Golda My-ass!