Questionnaires allow anonymity. In many surveys, honest answers depend on the extent to which the respondents feel the data remain confidential. Questionnaires without respondent names or location traces remain the best way to ensure such anonymity, with even the researcher not knowing the respondent identity.
Questionnaires also have an impersonal touch, as the researcher does not directly interact with the interviewee. This non-intrusive nature of questionnaires has its advantages for sensitive or controversial topics, in that the respondent feels free to make bold answers without embarrassment or fear or reprisal.
Such anonymity however also has a direct disadvantage in that the interviewer misses gestures, visual cues and subtle hints, which may be major sources of interpreting answers correctly. This lack of visual cues affects questionnaires that elicit sensitive issues or attitudes more than questionnaire that elects information.
The anonymity or non-interactive nature of questionnaire leads to increased chances of misunderstanding or miscommunication, as the respondents may interpret a question differently than what the researcher intended, with no chance to seek clarification or make amends.
Finally, the researcher has no way to ascertain whether the intended respondent or someone else completed the questionnaire.