95% of the pay a player will receive is through their "game checks." That is to say that a player signs a contract, and it will be broken down into 16 equal parts, with each one paid on the Tuesday after game day. They do not receive a check on a bye week.
Now, the other 5% is either in the form of a specific bonus or for their weekly salary during training camp. The training camp money is self-explanatory. The bonus money depends on the language of the contract. In most cases, that money is allocated into the 16 payments, so the players see it in installments. In some rare cases, its paid as a one-time bonus to the player. But that's the EXCEPTION, and most players don't see money like that in one check.
So for the "workout bonuses" that many players should be earning now, the payment would come during the season; they'd meet the goal of working out x days now and then see the money starting in September. So, in a way, they are not missing the money now. But they will miss it when the time comes, because they aren't able to work out to meet the criteria. It seems to me that there will have to be some language in the new CBA to cover this issue - if a player can't work out, but wanted to, and was to receive a bonus that was "likely to be earned" what happens?
Hope that helps a little.
Players aren't missing any money now, really. Because they wouldn't usually see a check now. But, they will notice it later when the game checks are smaller.