Het dierenpaspoort is volledig, behalve dat de vaccinatie ontbreekt.

Because dierenpaspoort is a het-word.

A useful rule is that in Dutch compound nouns, the grammatical gender usually comes from the last part of the compound. Here, the last part is paspoort, and paspoort takes het:

• het paspoort
• therefore: het dierenpaspoort

So even though dier is also a noun, the article is determined by paspoort, not by the first part.

Dierenpaspoort is a compound noun made from:

• dier = animal
• paspoort = passport

In compounds, Dutch often uses a linking form such as -en-, so you get dierenpaspoort.

This does not necessarily mean passport of several animals. It is simply the standard compound form here. Dutch compounds do this a lot, and the linking element is not always fully predictable from English.

So the safest approach is to learn dierenpaspoort as one whole word.

Because volledig is being used as a predicate adjective: it comes after is and describes the noun.

Compare:

• Het dierenpaspoort is volledig.
  Here, volledig comes after the verb, so it stays plain: volledig.

• het volledige dierenpaspoort
  Here, the adjective comes before the noun, so it usually takes -e: volledige.

This is a very common pattern in Dutch:

• De auto is nieuw.
• de nieuwe auto

Behalve dat means except that.

It introduces a whole clause, not just a single noun.

So in this sentence:

• Het dierenpaspoort is volledig, behalve dat de vaccinatie ontbreekt.

the part after behalve dat is a full clause:

• de vaccinatie ontbreekt

A helpful comparison:

• behalve de vaccinatie = except for the vaccination
  noun phrase only

• behalve dat de vaccinatie ontbreekt = except that the vaccination is missing
  full clause

So the presence of dat tells you a clause is coming.

Yes, after dat, Dutch normally uses subordinate-clause word order, where the verb goes toward the end.

In this sentence, though, the clause is very short:

• de vaccinatie ontbreekt

That is just subject + verb, so it does not look dramatically different.

You can see the subordinate structure more clearly if you add extra words:

• behalve dat de vaccinatie nog ontbreekt
• behalve dat de vaccinatie niet is ingevuld

In those examples, the verb part is clearly pushed to the end.

So yes, dat does trigger subordinate word order; it is just less obvious here because the clause is so short.

Ontbreekt is from the verb ontbreken, which means to be missing or to be absent.

So:

• de vaccinatie ontbreekt = the vaccination is missing

This is worth noticing because Dutch often makes the missing thing the subject of the sentence.

That is slightly different from how English often phrases it. English might say:

• the passport lacks the vaccination

But Dutch naturally says:

• de vaccinatie ontbreekt
• literally: the vaccination is missing

Another common example:

• Er ontbreekt een handtekening.
  = A signature is missing.

Because vaccinatie is a de-word.

A very useful pattern is that many Dutch nouns ending in -tie are de-words:

• de vaccinatie
• de informatie
• de situatie
• de organisatie

So if you see a noun ending in -tie, it is very often safe to expect de.

The comma separates the main statement from the extra exception clause.

Main statement:

• Het dierenpaspoort is volledig

Exception:

• behalve dat de vaccinatie ontbreekt

Dutch punctuation often uses a comma before this kind of added comment or exception, especially when the first part is already a complete clause.

So the comma helps readability and makes the sentence structure clearer.

Yes. Dutch has several natural alternatives, depending on style and emphasis. For example:

• Het dierenpaspoort is volledig, behalve de vaccinatie.
  = The animal passport is complete, except for the vaccination.

• Het dierenpaspoort is volledig, maar de vaccinatie ontbreekt.
  = The animal passport is complete, but the vaccination is missing.

• Alleen de vaccinatie ontbreekt nog.
  = Only the vaccination is still missing.

The original sentence with behalve dat is perfectly correct, but it sounds a little more formal or carefully structured than some of the shorter alternatives.