Does it matter CL9 or CL11 when selecting DDR3?

CL = Column Address Strobe Latency, which shows the number of clock cycles that pass from when an instruction is given for a particular column and the moment the data is available. In general, the lower the CAS latency the better within a given memory technology.

So, a CL-9 will be faster than a CL-11, all other things being equal.

Your motherboard's manual https://dlcdnets.asus.com/pub/ASUS/mb/LGA1150/H97M-E/E9092_H97M-E.pdf says not to mix memory modules with different latencies.

How much it slows down if you change to all CL-11 may not be noticed. A Tom's Hardware review showed a 2 % slowdown when CL-11 was tested vs CL-9, and that's before other hardware choices were factored in.

Since, with the 2014 design of your motherboard and its H97 chipset, at most you can run an Intel Core i7-5775C or i7-4790K CPU, so the difference won't be earthshaking, or even perceptible.

Is it possible to combine CL-9, and CL-11 on same motherboard ?

Yes; However, the highest latency module, will determine the latency for all modules installed in your system. This means all modules installed would have a CAS (Column Access Strobe) latency of CL-11. However, ASUS does not recommend you mix modules with different CAS latency, nor does ASUS explicitly indicate your motherboard supports that configuration.

Is my motherboard capable of running a module with a CAS latency of CL-11?

Memory compatibility with a motherboard is not determined by the CAS latency of the module typically.

Reference: CAS latency