As long as your OS and all supporting software are installed on the NVMe you will not notice any slowdown in the boot up process. Only when you launch the applications/games stored on the mechanical hard drive will the slow loading times be noticeable.
What I usually plan for is a big enough NVMe to install the run the most played games onto it. The games that you do not play so often can be installed on the mechanical HDD.
This does mean if your mood changes and you want to play one of the games on the HDD more you may want to consider uninstalling it from the HDD and re-installing it to the NVMe. Try with a single game and see if the speed of loading actually makes a difference to you. In a lot of cases the difference is not big enough to worry about.
NVMe's are reasonably priced these days with Amazon usually selling the WD Black SN750 500Gb just under $100 and the 1TB for less than $200 - have to monitor and grab once the prices dip tho so it does feel like the stock market when purchasing on Amazon!
Hope this helps you decide on how to configure your PC for the best possible storage option to suite your needs