I'll try to answer in a general sense. It appears that the Lufthansa engineers have changed only the interiors- basically they've changed the passenger fittings with the containment unit. As such, the effect of decompression will be the same as in commercial aircraft- in case of negative pressure containment unit, the air will tend to leak from it. In general, there are some safeguards in such cases:
By sucking air out through the filters, a negative pressure is created within the unit, so that while fresh air may leak in, contaminated air will not leak out. An alarm sounds if negative pressure is lost.
... in case the negative pressure protection failed, the air inlet at the front (crew-facing) side of the tent is also fitted with a filter to prevent airborne contamination of the main cabin. As a further protection for the crew, Phoenix Air’s mechanics have reversed the airflow in the whole aircraft, so that now it flows fore to aft (instead of aft to fore as it comes from the factory); the pilots and medical crew are in effect located ‘upwind’ of the patient.
However, as @abelenky already noted, in flight decompression is quite rare and the people on board have to worry more about the patient they are transporting than decompression.
Negative Pressure tents with HEPA filters are usually used only in medivac cases where the diseases are highly infectious. In other civil medivacs, the patients are usually exposed to the cabin.
There is a FAA approved Aeromedical Biological Containment System (ABCS) devised by CDC and used in US, which uses the same negative pressure principle- so I'd say that it is safe to operate.
For medical aircraft, the cruise altitude is usually set lower- FL200 or so to enable having the cabin pressure altitude at a lower level (for military aircraft, it is maintained at 4000', though it can vary depending on the circumstances). One thing to note is that most medivac aircraft are business jets like Gulfstream and Learjet, which can maintain sea level cabin pressure upto FL200.
Also, any interior modification will have to be approved by the corresponding regulatory body (here its EASA, though I'm not able to find anything about this particular aircraft). Other manufacturers have obtained EASA certification for negative pressure tents and as already seen, FAA certification too.
European Air Ambulance explains the EASA certification process for medical aircraft, which basically involves:
Type certificate for the original aircraft
Supplement Type Certificate for the medical configuration and
Air Operator Certificate for the aircraft equipped with the approved medical configuration.
Image from European Air Ambulance