1) Allowing only a limited number of players, that had been part of a team that "had gone" BOT, to be part of the NT.
i believe every draft you won't get an unlimited amount of draft pick at one bot, even two would be pretty much and three the max.
2) Better monitoring, for identifying, which team actually played, and who had cheated.
Generally, there is a "cheaters mechanism", and it is OK.
In addition, I believe that the argument of cheating is general, and hence no need to focus only on NT.
i don't believe much at the cheating strategy bring in here too, but it works more like that, lets say Nation a have three divisions where the first too would be pretty full. If now preseason they are registering some teams that the 3 league has some human controlled players, this country get a fourth league as puffer. Which means they get 64 draft pool, for their NT.
In germany this might be even bigger prob, since we have four active league, and a sixth division.
Which means:
1 + 4+ 16 +64 = 85 normal draft classes(and you might point out that some of the foruth div classes could get in the next group)
256 + 1024 = 1280 draft classes who put their biggest talents on free agency.
So the pool of trainable player will increase heavily and make scouting a bit stupid cause you could buy good talents for very small money.