Not clearing a road means fewer people use it, but you not going out with a shovel to clear a public roads isn’t you discouraging their use nor is you canceling your plans to clear said roads.
Having zero subsidies is the default situation.
If Amazon delivered you a TV yesterday that doesn’t suddenly become the default where you can expect another one today and every day after that.
The US government does a new budget every year, making every year a new ballgame.
And my point about there being no natural state of subsidies is more important.
So if your argument is some subsidy will probably happen next year sure, but individual subsidies change over time. No specific subsidy is the default.
For any specific situation the default is no subsidy.
With millions of situations some of them are not going to be at the default.
In 500 years will some specific things be subsidized? Vs in 500 years will something be subsidized?
If the end result of removing this exemption is that there is less R&D done in the US, then yes, empirically, removing the exemption discourages R&D. Assuming the mass layoffs were indeed fueled by the removal of this exemption (I don't know if the article is correct or not), then it is reasonable to assert that it is true that removing the exemption has reduced the amount of R&D done.
Or, you could also say that the "default state" is some low level of R&D, and the tax exemption encouraged and incentivized more of it.
Either way you slice it, though, the status quo prior to 2022 was some level of encouraged/incentivized R&D. That status quo changed to encourage/incentivize less R&D, and companies have followed these lack of incentives and have fired a lot of their R&D staff. Is that a good thing for the US? I can't see how it could be.