There are two Pirates in Baseball America's new Top 50 prospects list - Neil Walker at #43 and Andrew McCutchen at #50. (BA ranks Tom Gorzelanny #98.)
These rankings are a lot kinder to the Pirates than many other recent prospects lists (Baseball Prospectus', Dayn Perry's, Wait Til Next Year's), but even if we assume that kindness is justified, three prospects in the top 100 and none in the top 40 isn't nearly enough. As WTM points out, the Pirates always choose in the first half of the first round, when many top prospects are drafted. Of BA's top 20 prospects, 16 were drafted in the first round. (Two were drafted later than that, and two were international signees.) Ten of them were drafted in the first half of the first round. While the Pirates didn't have the opportunity to draft all those guys, they could have drafted many of them, and keep in mind that the Pirates' own recent top draft choice Byran Bullington isn't on the list. Also, the Pirates are always acquiring prospects in trades when they dump veterans.
It's true that the Pirates have recently promoted many players to the big leagues, keeping those players from being eligible for prospect lists. But except for Zach Duke, none of them are especially likely to be an impact player. And Duke was drafted not by Dave Littlefield, but by Cam Bonifay.
Hopefully, Walker and McCutchen will have strong seasons and move further up the list next year. If they don't, though, it's not likely the Pirates will be well represented on lists like these next year, either.