The fact that you do not have your passports does not mean you will be denied citizenship, so while missing those documents is certainly an inconvenience (possibly a major one), it is not a insurmountable problem.
If you really can't find the passports you'll have to make a declaration that they were lost (if they were expired I'm guessing a notarized statement is likely the way to go, as police probably won't create a report for loss of an expired passport, I expect), and include a photocopy with your application.
You will need to have a list of all the trips you made to be able to complete the physical presence calculator. If IRCC deems your application unreliable because you did not include all trips you made, you are more likely to undergo close scrutiny and may have to prove your presence. There is a chance, because you do not have your passports, that they will ask for this kind of information anyway. There is a
thread describing the kind of information IRCC may ask for in such cases.
You can start gathering that information just in case they ask for it. If they do, you have the information available. If they don't, you may have spent some time and effort unnecessarily. That's your call to make.
If you've only travelled to the US your entry/exit records should be available to them (as you'll permit access to CBSA records). It is possible to make a FOIA request to get your travel records from CBP, which could be another bit of documentation you'd have available. You can request CBSA records if you need them for yourself, but note that there have been multiple reports of trips being missing from this report (so this should not be your the basis for your physical presence calculation, it can be at best a corroborating piece of information).
Gathering booking confirmations, credit card/banking records,... may all be useful to document the trips you made. If you do not have a reliable travel journal you should cross-check as many sources as you can to create the list of trips you made.
Don't submit any information beyond what is asked for with your application. You would need to include a letter about the lost passports, of course, but any extra information you do gather should only be sent if/when it's asked for.