The CIC will not punish you for the shortcomings of the CBSA reporting system. They are aware that there are sometimes missing entries.
You're right that it's important to be honest on applications*, but it's not true that all govt agencies have access to all records. Agencies only have access to their own records because of privacy concerns. The CIC only has access to CIC records. The CIC requires your permission to access your CBSA records (hence the checkbox on the application.)
The CIC is not in the business of punishing or passing moral judgements on applicants. They are in the business of seeing whether applicants have met the qualifications for immigration or citizenship. If an applicant presents a lot of contradictory information or certain specific triggers, they will ask for more information in the form of RQ. This is not because they assume the person is a bad person (bad people have a right to citizenship as long as they meet the qualifications), but because they want to see if the applicant has met the qualifications.
The CIC doesn't have access to banking, financial, educational, tax, work or border records. They make the applicant get it, or they ask for permission (in the case of CBSA reports).
*The one exception to being honest is if an applicant came to Canada as a refugee and traveled back to their home country at any point. If that is the case, it's important to talk to a refugee lawyer before sending that information to the CIC because one's right to remain in Canada could be at risk.