Losing draft picks in baseball isn't quite the same as in football or basketball. I just did a quick look back over the Astros history. They have never had the all their players drafted in the first three rounds make it to the pros. The two times they had 100% make it were 2007 when they lost their # 1 & #2 picks and their #3 made it but not with the astros so he didn't sign. The other was 2003 when they had no #1 but #2 & #3 made it but #2 was Stubbs who didn't sign with the Astros. So no real 100% drafts.
There were 7 drafts were none of the players drafted in the top 3 rounds made it to the majors (72, 73, 81, 99, 06, 09, 13 so far anyway but two were traded away).
The worst was 91. The Astros had 8, yes 8 picks in the first three rounds. Only one player made it to MLB. That was John Burke with a career war of -0.5. So yeah, that draft sucked.
So I don't know how much it hurts the Cards but I think it helps the Astros because the more picks you get, normally the more chance you have of finding a solid player.
The Astros had a good run in 10 (3/5), 11 (2/3) and 12 (3/4) and have already had 1 each make it from 14 & 15.
So this year, the Astros will have 5 picks in the first three rounds. They have had that # in 89 (4/5), 94 (4/5), 05 (3/5), 08 (2/5), 10 (3/5) and 15 (1/5 so far). If they can get 3 out of the 5 to the bigs, it will be a successful draft.