I don't follow e-sports, but it would seem like it will be harder and harder to prove top players don't cheat in games that partially rely on speed/reflexes as better scripts evolve. Seems like a thing games just have to deal with and also why things like mobas aren't all that fun to begin with.
That's actually very easy, since all serious esports have "offline" competitions (offline meaning in-person at venue, since most games don't have true LAN anymore due to piracy stuff. It still is "online" but you get the point). The tournament organizer can ensure the default client is installed and no additional mods and stuff are being used.
The actual issue in competitive gaming that will continue to be a problem for a long time is of course any online competition (some games have better anti-hacks than others), and match fixing or agreements between the players.
Match fixing is like any other sport with match fixing. Most notably was Ma Jae Yoon, korean starcraft:brood war progamer who arranged for players for throw matches so that gambling websites can place large bets on the outcome.
Agreements, as I refer to, is a bit harder to prove. For instance, say there is a $X USD prize for first place and $Y prize for second place. Players have, and allegedly have in other cases, agreed that they'll just split the money evenly (X+Y)/2 regardless of who wins in an under-the-table deal. This is particularly possible to happen since many esports competitions nowadays are "top-heavy" prize distributions, often the majority of the prize pool solely in the first place prize. E.g. first place 5000 USD, second place 500 USD. You can't make a living making 500 USD every few months. You can do that winning 5000 USD occasionally.****
There also is obviously match throwing/etc to get more favorable brackets or in group-stages that are like round robin and your teammate is in the group as well.
But those issues are common to every competition that has enough money to entice people to cheat but not enough money to just make big $$$ off of your salary where the risk of getting banned deters many people or you have an organization that thoroughly investigates potential cheating
Of course, that does not stop some no matter how much money they make. Like all famous match fixers of any sport or competition. And obviously, basically no sport has a real solid definitive regulatory/investigatory board, particular when it comes to things like recruiting rules and salary caps and money under-the-table that doesn't directly impact on field performance. It is easier to test for steroids than it is to necessarily find that 20,000 "bonus" given to a college athlete's uncle or whatever scenario you want to extrapolate.
****edit: well I say that because there is generally more allegations for that medium range of money, but it doesn't matter how high the prize pool goes. Just there is probably higher scrutiny.
Esports also currently suffers from many shady business deals and tournaments not paying out prizes. It steadily is getting better, but it depends on the game and is case by case. Several professional gamers are "owed" severals or tens of thousands of dollars from their teams that never payed salaries, or tournaments that are basically never going to pay out their prize pools, etc. And you are relatively powerless to do anything about it, if say, a german tournament you went to owes you 2000 dollars for winnings + travel they said they would reimburse and you are some chinese player. You're never going to get that money. [that was strictly hypothetical]