It's not as big of deal as people make it out to be. The talent presently in their system isn't comparable to say 2012. The thing about top 100 lists is they are purely about upside. They don't really measure depth. For example, Kyle Hendricks never even came close to top 100. If it went to top 200 he might not have made it. Contreras hit .242/.320/.359 in 2014 was rule 5 eligible and anyone could have had him, then went out and hit .333/.413/.478 in AA in 2015 and suddenly was a top 50ish player. That's the other thing with these lists. It really only measures 2 groups of players. Either A) really high draft picks(Royce Lewis is #20 and MacKenzie Gore is #19) or it measures guys at AA/AAA. There's occasionally some exceptions to that such as super high profile IFA's like Vladdy Jr and Eloy/Torres were but by in large players don't really get noticed until A+ and unless they are nuts there don't get ranked until AA.
If you look at the top prospects the cubs have right now they are in some order, Oscar De La Cruz(might be AA but he's been hurt so it's difficult to put faith in ranking him), Jose Albertos(probably starts next year in A), Adbert Alzolay(kind of a one year wonder but he'll be top 100 if he proves it through midseason next year), Alex Lange/Brendon Little(both probably at A and not high enough picks to get ranked right away), Aramis Ademan(likely goes to A+ and he's only 19), Nelson Velazquez(maybe A ball if he's lucky but probably ex st/a-), Victory Caratini(top 10 catcher but not enough upside for the top 100), Thomas Hatch(likely just going to AA), and Jen-Ho Tseng(likely AAA).
So of the top 10 guys the cubs have you have Alzolay, Tseng and Caratini who've played enough to warrant consideration but Tseng and Caratini while good prospects don't have huge upsides and Alzolay doesn't have a proven track record. The majority of the talent left in the system is just at too low a level to warrant consideration right now but it's not like it doesn't exist.
Also for what it's worth there's a bunch of really intriguing guys the cubs have between DSL, rookie league, A- and A ball that people don't really know about yet. For example has anyone besides me ever heard of Fernando Kelli? He's a 19 year old CF the cubs have in DSL who hit .320/.437/.443 with 11.9%/17.1% bb/k rates and stole 58 bases. He's maybe a year behind super elite IFA signings as they generally get to mesa by 18 but given how well he hit last year he might be able to get to A- this coming year which would make up about half a year and he'd more or less be on par with all but the most advanced IFA's in his age range.
There's more guys like that but a lot of it is just people putting together the collection of tools they have. If they do they become a good prospect such as Alzolay did last year. I have more faith in the cubs scouting/development of hitters so with a guy like Kelli if they like him I have a pretty good assumption that the guys going to hit. Pitching thus far has been spotty with them though they have drafted more low upside college arms so that's not entirely surprising. And another thing to remember is they get back into the IFA game this july. I'd expect to see them land some big names because near as I know they didn't even remotely sniff any of the Braves IFA's who got released by MLB as punishment. In theory the cubs could have used money from next IFA period to sign them but they didn't which tells me they likely have some big guys already agreed to.