As for #1, perhaps but he's being payed pennies and that's where the value comes in and why teams want him. He made something like $2 mil last year. A league average player in FA is making $8-10 mil. Ryan Ludwick got a 2 year $15 mil deal last off season and wasn't any where near the player Schierholtz was.
As for #2, again, money comes into it. Shields made $9,000,000 this year. Shark made $2,640,000 this year and predictions for his arbitration next year will be in the $5 mil range. $4 mil doesn't seem like a ton of money but it's another player. And when you have teams such as the pirates and KC who have reported interest, $4 mil is a lot of money to them especially when you consider alternative solutions. Take Dan Haren as an example. You'd likely consider them similar pitchers. Haren made $13 mil this past off season. And that's before you even consider that many view Shark as someone who's yet to reach his full potential.
So yes, I think 3 high value prospects for those 2 players is warranted especially when you consider there are multiple reports of different teams wanting both. Also, in some regards you're over valuing prospects. The entire point in trading 3 for 1 or 3 for 2 is that prospects are a gamble and don't always turn out to be what people expect. In the top 4 cubs prospects many expects at least 1 to fail and they are top 50 players. Skaggs + 2 guys outside the top 100 is even more likely to have someone fail.