Theres a big difference between a single instance, and whats normal. Meta Knights can beat Snakes. However, Snakes usually beat Metas.
Its not all about match ups either. Dedede is winning a good number of tournaments, yet he has a disadvantage to half the cast. Theory only goes so far. Player skill is also a factor, which is why 1 tournament doesn't decide anything but the results of that tournament. The people who play Snake are going to know how to deal with Meta. Meta's will know how to deal with Snake.
If Meta Knight were as broken as you seem to believe. He'd have been banned. As it stands, he has 5 neutral match ups (2 of which are against bottom tier characters), and 2 disadvantaged match ups against Snake and DK. This is simply by character ability. Taking into account if 2 people of equal skill are pitted against each other. Snake Vs. Meta for example, Snake is going to win the majority of the matches. If you were to pit two people of unequal skill, say M2K against myself. I'm probably going to have my ass handed to me regardless of whom I chose. Theres also factors such as horrid mistakes, human error can sway a match just as easily as uneven skill can.
One tournament decides nothing. 30 at minimum is the statistical magic number at which normality can be seen from.