Officials at NASA were caught unaware by the announcement on Wednesday evening. They had been expecting the existing acting administrator, Janet Petro, to remain in place at least through the end of the year while a new nominee was put forth to lead NASA and confirmed by Congress.
Sources indicated that although Petro did not have a particularly high standing within the Trump administration, she did nothing to be removed from her position. Rather, it seems that Trump wanted someone he liked and trusted running NASA. This is probably a benefit for the agency, as it will give NASA a direct line to the president. For example, Duffy can text Trump if NASA needs something or is being treated unfairly during the budgeting process.
Petro did not have that kind of political sway, and this is a White House in which access to the president matters a great deal. The agency was in great peril, as there was no one in headquarters who could push back on harmful things being done to NASA or get things done. Duffy will have that kind of pull. But he will also be incredibly busy already with the Department of Transportation.
There are also some reasons to be concerned about NASA under Duffy. Because he does not come from a space background, but rather a political one, Duffy likely views his mission at NASA as carrying out the vision of the space agency established by the president's budget request, which slashes funding for science and makes significant changes to NASA's deep space exploration plans.
NASA finally has some clarity on who will lead the agency over the next several months, and it is a person trusted by the president. Duffy is also viewed as a capable leader and experienced politician who understands how Washington, DC, works. It's possible that Duffy will listen to the concerns of leaders at NASA in the coming weeks and seek to offset some of the more Draconian (and difficult to understand) cuts by Vought's office.
However, it is also possible that he takes his mandate to slash NASA's budget and workforce seriously, and in doing so would be vastly more effective than Petro.