My wife is presenting in a conference in the USA (she doesn't need a visa to travel under the visa waiver program). I'm accompanying her but I don't qualify for the visa waiver and will need to apply for B1/B2. The hotel reservation is in her name only, but obviously we are traveling together and staying together.
Is hotel reservation in her name enough proof of accommodation for my application? I'll be providing of course proof of relationship, conference details etc.
As annoying as is it that all US visa applications must be done in person, this is one of the benefits of that - you have a good opportunity to explain things like this during the interview!
I would suggest taking along a copy of your wife's passport (and if you do not share a common surname, proof that you are married such as your marriage certificate), along with the hotel reservation. If the consulate staff question the fact that the reservation is in "someone elses name", then it will be a simple matter of showing them these documents to show that you are sharing with your wife.
Many hotels will allow you to add a second name to the reservation, and whilst it might not hurt to do this it's extremely unlikely to be necessary as far as the visa application goes as long as you can provide documentation like that mentioned above.
So in short, no, this is not likely to be an issue at all for your visa application.
