Jumper headers are quite often missing, they are for example for PCB traces which you can cut manually and replace with a header (which for example can be used to measure supply current). I don't have it myself, so dunno what the resistors and capacitors are for, but it happens more often in the final version stuff is removed.
Can it reach the speed it should be able to reach? Yes, on its internal oscillator with PLL enabled. Does it currently do it? No, it looks like ST has been a bit lazy with proper support. It is being added slowly by community members who have it, but imo it should have been there from the beginning.
There is for me also one-big 'if' regarding the crystal removal: the microcontroller has a USB peripheral. But does the crystal provide sufficient accuracy to actually use it? (Although I don't even know if the relevant pins are available). (This is unrelated to the programmung USB port btw, if that also doesn't have a crystal then it should still work for the F401, as soon as there is USB code).
Whenever I hit compile in my browser (I tried IE, Firefox, and Chrome) it just downloads a .bin file but how do I actually deploy the code onto the device?
In addition I just received my Nucleo board today and it missing several SMT components. Not sure if they are supposed to be missing maybe they were determined unnecessary after manufacturing or something or maybe my board is just a dud. I bought if from Mouser so I suppose I can get somewhere with their support but I wanted to make sure the parts were supposed to be there first.
I am missing crystals 2 and 3 as well as probably 10 surface mount resistors and capacitors. That just seems so wrong to be but who knows.