Broadly speaking, a Ministerial Direction (MDs) is a written instruction from a minister to a civil servant or to a government department. It is not a statutory instrument, and so does not constitute legislation.
The normal usage of an MD is described by a Commons Library briefing paper like this:
If a UK Government Minister decides to instruct a Departmental Accounting Officer (a senior civil servant) to proceed with spending, contrary to the advice which has been given by the Accounting Officer, the written instruction is called a ministerial direction.
The list of all such MDs shows that they are normally in the form of a letter from a minister to a civil servant (example).
However, the specific MD mentioned in the question is not an MD of this type, and (at the time of writing) appears to be unique, being the only one listed on legislation.gov.uk. This may be because the power to make MDs are not normally specified in legislation, but are a normal part of intra-departmental communication.
In this case, the MD is still an instruction from a minister to a civil servant - in this case the King's Printer (an office held by the Controller of His Majesty's Stationery Office) - but the power to do is specified in the European Union (Withdrawal) Act 2018.
It may be that the power to make this unique kind of MD is specified in legislation because it relieves the King's Printer of a statutory duty (in this case, it removes a legal requirement to publish certain EU legislation), which is not true of normal MDs. Equally, it may have been kept as an MD, and not an SI, because it again remains a matter of communication within government, for which an SI is not necessary.