How will the academic boycot of Israel (BDS) influence my career if I get a PhD in Israel?
If there is going to be a problem, then it will occur when searching collaborating institutions outside Israel. I know there has been talk about stopping such collaborations. However, how much that has been implemented is another question. In my field (quantitative sociology) that has not been the case. The argument being that you are not going to help solve a conflict by closing down channels of communication. This is not the place to discuss the merits of that argument, but you can imagine that such an argument is popular in academia. So I suspect that it should be possible to find a collaborating institution if you needed one.          

I don't think you have to worry about the value of your PhD. That should be recognised outside Israel without problems.