No, the Master's degree quota is unaffected by this legislation. The version of the bill presented in the previous congress is here:
https://www.congress.gov/bill/114th-congress/house-bill/5801...I expect the language of Rep Issa's bill for this session Congress to be largely unchanged.
"Exempt" H-1B employees are not counted when determining whether or not an employer is H-1B dependent. Generally, an employer is H-1B dependent if over 15% of their employees are nonexempt H-1Bs.
The old criteria for exempt status were:
(a) at least $60k annual salary
OR
(b) Master's degree
The new criterion proposed in the bill is:
(a) at least $100k annual salary
This explicitly targets companies like Infosys, Tata, etc. who use hordes of H-1Bs but pay them just over $60k or ensure that they have Master's degrees.
Microsoft, Google, Amazon, et. al. will still be able to employ hordes of H-1Bs but they will be unaffected due to the high paying nature of the work.