IPUMS USA and IPUMS CPS use the Public Use Microdata Sample (PUMS) files released by the Census Bureau to offer harmonized versions of the data files. We do not remove any records from the ACS or CPS PUMS files.
The ACS PUMS microdata itself is a subsample of the full ACS microdata collected. The ACS PUMS includes only about two-thirds of the full ACS sample used to produce official ACS estimates (these summary files are available via IPUMS NHGIS). Regarding the CPS, I am unable to find documentation that notes that the CPS PUMS is a subsample of any full CPS file. However, I do know that cases in the CPS PUMS have their ages perturbed and some geographic identifiers are additionally synthesized to further protect confidentiality.
Our default data format for custom data downloads from our website rectangularizes data onto the person record, meaning that any household-level variables will be appended to the person record (and all persons within the same household will have the same values for these variables)–as a result, these custom download files will omit records for households without any person records (i.e., vacant households). To include empty households in your custom data request, you will need to request either a Hierarchical or Household records only data structure for your data files.