Sorry, you are simply incorrect. While the intelligence budgets are not public, the appropriations are included under the defense appropriations bill.
Here is a primer from the Congressional Research Service on the intelligence budget:
From the summary: “Over 90% of intelligence appropriations are included (or “hidden”) within the budget of the Department of Defense (DOD).” This includes all of the appropriation for the NSA.
There actually has been a long running parlor game amongst defense journalists who comb through the defense appropriations bill and try to back out the obscure line items that are going to fund black projects. This is how we have estimates of the intelligence budgets.
In summary, the NSA appropriation is covered by the defense appropriation bill and, yes, this amendment would limit the ability of the NSA to spend its funds on these programs.