In terms of cheats like scripts and speedhacking, I've personally almost never seen them. In the few instances I did find suspicious (mostly in earlier seasons), the players who may have been using those exploits were often compensating for their own lack of skill and game sense. On balance, it didn't seem to help skew matches in their favor--it was just annoying (and even exploitable, in the case of scripting).

As for wintrading, it's also fairly rare, but even in cases where players were obvious about it (one person repeatedly throwing for another on the same job), moderation has been spotty. It's more often the case that people report the offending parties en masse and nothing happens. Moreover, there's a grey area--someone doing 0 damage and healing in a crystal-rank game is obviously up to something, but a more moderate amount of sandbagging comes with plausible deniability. Are they throwing? Or did they just decide to queue up drunk on a whim? Is it coincidence or conspiracy? Say there's 10 players in queue, with one good MNK and one bad MNK. You might be able to prove that the good MNK is benefitting from putting the bad MNK on the opposing team, but you can't prove they're working together. (They often aren't, I find.)

There's also the matter of deliberate sabotage. Rather than throwing games to benefit an accomplice, there are some players who throw games to spite people on their team they have a grudge against. Moderation is also near-nonexistent on this matter.

The low player population and lax moderation creates a game state that can be manipulated by those with bad intentions. Even so, the vast majority of people just want to play the game, and the vast majority of the leaderboard in any given season is legitimate. If you want to grind ladder, you shouldn't let the few bad actors discourage you. If you're skilled, you'll climb.

These problems would be alleviated if we had more players in queue. Combined regional data center queues in 7.0 please ;-;