It may not be in my best interest to ask a professor I have done research with for recommendation letters. Can this seem suspicious in my application? I am not from the US and my field is in the social sciences. A while back, I started collaborating with a foreign professor on a research project which is now under review and another one which is halfway through. however, I did not find these topics very fulfilling and I want to move to another area closer to my original interests (I already have two other published papers relevant to this new area). The complicating issue is that the professor has told me several times he would be very interested in having me as a PhD student. So, I guess, he may not appreciate the fact that I have decided to pursue another area with another supervisor. Therefore, it may not be very fair or wise to ask him for letters of recommendation. What worries me, however, is that if I list these papers in my CV (which I eventually have to when they get published), it may raise questions/suspicions about why I have not asked him to recommend me. I cannot preemptively tell my prospective supervisor or the admissions committee the real reason for my reluctance to ask this professor. So, I am concerned that if such questions arise in their minds, it may lead them to mistakenly assume that I have something to hide, motivating me to exclude this professor as a potential recommender.
Is this a legitimate concern?
the professor has told me several times he would be very interested in having me as a PhD student. So, I guess, he may not appreciate the fact that I have decided to pursue another area with another supervisor

Could be, if this person is vindictive and unethical. But if they are a decent human being they would write a gushing letter about how they would love to have you as a student, and other professors would take this as a good sign.
Unless you have a stronger reason to think this person falls into that bad category, I think they are probably one of your best potential letter writers. Someone who wants you as a PhD student is someone who has confidence in your research potential - that's exactly what you want from your letter writers.