It is grammatical. You can use it as many times as you want.
However, you should avoid using the same word over and over again in writing works such as journals, articles, and essays because, as a reader, it makes me feel a little bit uncomfortable. I feel that the sentences that use some particular words for too many times make me read it not as smooth/flow as it should be. It is acceptable in sentences that emphasize some certain actions so you say it repeatedly like "I kicked it, and I kicked it, and then I kicked it again.". That makes sense because you are trying to show that you really kicked it three times. But for this particular case, I suggest you change the second where to "the place" instead. Therefore, It should be like so.
"I just hope that, in the country where I have applied to work in the future, is the place I will find my soon-to-be wife, so that I won't have any problem as for the long-term relationship issues."
In addition, I personally would remove the commas (,) when I use the word that but I don't know the reason behind it. Thus, it can be like this.
"I just hope that in the country where I have applied to work in the future is the place I will find my soon-to-be wife, so that I won't have any problem as for the long-term relationship issues."