The first question is whether you even have the option of working on both degrees at once. I'd assume you don't, since positions with full funding are generally based on an assumption that you will be devoting full effort to them. They may formally rule out other employment/studies, and even if they don't the department may become upset or feel tricked if they discover you are also doing something else at the same time. (And departments can sometimes react similarly even if the position has no funding: even if you are paying your own living expenses, they probably consider themselves to be at least partially subsidizing the costs of your education.)
So you shouldn't try to do both degrees at once unless both departments officially agree to it. Even in that case, I think it's a bad idea. Success in graduate school is based on quality, not quantity, and this approach can't be good for quality. You'll be writing your thesis remotely, with far less contact and advising than you would have had in person. That alone will make it harder to do your best work, but at the same time you'll also be participating in a different full-time program. You might not be able to do good work for both at once; if you can, then you ought to be able to do great work if you focus on just one (and doing great work at one program is much better than doing good work at two). The same reasoning applies no matter how talented and hard-working you are: if you can do great work in both programs at once, then you ought to be able to do amazing work by focusing on one.
If I do have two MSc degrees in the same subject, would is have any negative or positive effect on applying for a phd degree later?
Having two MSc degrees might be a small negative, by making you look unfocused, but it probably won't make much of a difference either way. Ultimately, you'll be evaluated by your academic achievements (papers, thesis, outstanding performance in courses), judged primarily by quality rather than quantity, so you should try to maximize these achievements.