Turning off "Don't Import Suspected Duplicates" by default?

The Import Preset handles that. So, you need to switch the option off and then update your Import Preset to make that option default.

On a personal note, I agree with @cmgap, @DdeGannes and @dj_paige : not importing duplicates is an asset, and you should, as @cmgap suggested, look carefully into this to rule out other issues. Duplicate photos in your Lr database can be confusing when searching a certain picture or edit. I use the powerful collections, to manage my data according to different criteria. And my Lightroom database is my primary tool to manage photos. I do not touch-up photo data outside of Lightroom.

When you import a image file into LrC the info about the image file's location and all work and edits you perform with that file is automatically stored in the LrC Catalog file. When you store copies of the specific file in another disk / folder location and import the file again then when you make new edits there will be confusion within the catalog data. No problem if you import a copy into another Catalog.

Better to maintain one Catalog with one original image file and utilize virtual copies feature in LrC to have several edits with different settings/ edits applied. Just a thought.

One way is to create an import preset with the setting turned off and ensure that you use the preset whenever you import.

It's odd that you say that you always have to turn it off though because it is a sticky setting and it will remain on the last state is was in until you physically change it. Please provide more details on mysteriously missing files... Lightroom Classic's import functionality while not flawless is reasonably straightforward and Do not import suspected duplicates is a valuable feature. There may be other reasons for your missing files.