Who gets hurt? The high school and college players who were good enough to get picked in the range of Rounds 6-15. They didn’t have a voice here because they aren’t one of the two sides at the negotiation table. That trickles up to the lower levels of the minors, too, which usually see an influx of brand new talent to the lower levels after the draft. What will Rookie Ball look like? Short-season teams are generally stockpiled with draftees. 
For now, the owners have saved a lot of money by significantly shortening the draft. 
As part of the agreement, teams can sign an unlimited number of undrafted free agents for ,000. 
For example, the slot values in the sixth round last season were between 1,600 (pick 168 overall) and 7,000 (pick 197). Now the players selected in that range could be pursued by teams for just a small fraction of the cost. Even the last pick of the 10th round carried a slot value of 2,200, so teams have saved some money here, though a drop in the bucket compared to what they are worth.  We might not have minor-league baseball this season at all, though, so maybe the latter point is moot. We’ll see. 
The reason for the drastic reduction in the number of rounds is for the owners to save money. Due to the coronavirus shutdown and then opening the eventual season — and likely playing for a while — in front of no fans, they are set to lose out on a significant stream of revenue here in 2020, so they wanted to find ways to cut costs. An easy place to look that current players wouldn’t be overly averse to the amateur pool from which the draft draws. 
After weeks of speculation and reporting, Major League Baseball has reached an agreement with the players that the draft will be just five rounds this season. The draft has for the past several years been 40 rounds. Both ESPN and The Athletic reported the deal as finalized Friday evening.