Overall depends on the following (for me);
- Will I also be maintaining this solution?
- If not, are the people that will maintain the solution also comfortable with Custom API calls?
- Can we achieve what we're doing with the native modules?
- Is it an unsupported action?
- Are we creating/updating many records at a time (definitely better to use Custom API calls in that case and build a pattern that will impact up to 100 records per API call)?
- How large is the system?
- When working in Fusion it takes a few seconds - sometimes a bit more than that - longer to load native modules like Search or Create, and this can be longer if there's more to load ie thousands of custom forms to select from: the Custom API call module will always load in a couple of seconds or so
Also typically default to Custom API calls but it's a double-edged sword; you can build using patterns that aren't achievable with the native modules, but you need to get your hands dirty and transfer of maintenance can be a bit trickier depending on comfort levels.
Native modules are more user-friendly and sometimes though it looks like one simple action it's actually performing 2-3 different api calls in the background (take the Convert to Project action as an example, or Download Document).
Will it impact performance using native modules? Not really. Might just take longer to open those when making edits as it has to retrieve more information to show you than the custom API call modules.