There is noting wrong with two of them having HMO licences, the local council must have agrred and they carry our rigorous checks.
And the guests are renting the rooms - if no services are provided, and they share kitchen and bathroom facilities OR have access to their own on a studio type basis - and they fulfill the remaining remit as detailed, then the status of the building is correct.
Is breakfast supplied, sheets changed? Rooms cleaned for the guests ? That is the main determination that is looked for in a guest house situation.
But whether trade or rental income - the income tax/corporation tax would be the same its just the VAT sitation that I can see concerns you
Even if they stay just one or two nights IF NO services are provided, then its just rental income - the HMO determines the size of the property the layout and what facilities are shared
Link here for Government interpretation of HMOs
But if truly a HMO then VAT should not be claimed from these buildings -
Does that help?
Let em know if I can assist further