Lack of membership in other parties
About two thirds of the Dutch voters are a "floating voter"
(Dutch: zwevende kiezer), meaning they don't have any particular party loyalty
and could vote for one of several parties. In addition, only about 2.2% of
eligible voters are a member of a political
party.
So as you can see, party loyalty among the general population is low, and has
been in decline for decades.
But for the SGP party loyalty is much higher. For SGP voters, it's not just a
political party, it's a religious affiliation. The majority of SGP voters are
from the bible belt or
otherwise geographically clustered. See this chart of SGP voters:

The SGP is the only conservative protestant party to represent these people. The
other Christian party, ChristenUnie has a much more progressive and social
party program, and the Christian Democrats (CDA) are not all that Christian
(similar to the Christian Democrats in most countries).
So this is reason one why the SGP has an unexpected high number of members:
sharply dropping memberships in other parties, which is not happening – or
happening less – in the SGP due to higher party loyalty.
Demographics
The second reason is that the demographic are a bit more involved than just
"religion is in decline".
Don't look only at the relative numbers of religious participation. It's
true that support for the reformed denominations have decreased from 37% in 1960
to 18% in 2015 (cbs),
but the population has grown as well. In absolute numbers
we're going from 4.2M to 3.1M. Still a loss of well over a million, but much
less than 3.2M if we had forgotten to scale the population down to 1960 levels.
Secondly, some of the more conservative regions have a larger – sometimes
spectacular – population growth. Look at this map of family
size,
then look back at that map of the SGP voters. See similarities? Not an exact
one-on-one match, but it follows the "bible belt" pretty closely.
The population of the Netherlands in general has grown by about 40% since 1960,
but for some conservative regions this number is much higher. In Urk the
population has grown by 400% since 1960. If we consider that about 50% of voters in Urk vote for SGP, then this translates to about 4,000 extra SGP voters,
quite a few of them will become members.
This also explains why the electoral result has been stable at two or three
seats for almost a 100 years. For the upcoming March elections the SGP is
currently polling at four seats!
Young deciders
All of the above applies to the SGP Youths as well, but for the Youths I would expect the
relatively high number of members to be even more pronounced as young adults raised
in a religious family and community where >20% of the population vote for the
SGP tend to have pretty clear views on their political and religious
affiliation at a relatively young age, whereas other people tend to choose
their political affiliations at a later age (if they ever choose one).
Alienation from the rest of the country
This last reason is a bit more subjective, but in my observation it seems to be the case that
religion in decline tends to increase religious participation.
The religious population will feel alienated from the rest of society when it
moves in directions they oppose. This is particularly the case in the
Netherlands, as it has one of the most liberal policies in the world: legalized
euthanasia, gay marriage, soft-drugs (sort-of anyway), abortion, prostitution,
etc.
You can see this in some of the values the SGP is trying to defend. A few years
ago the SGP fought tooth and nail to maintain the anti-blasphemy laws. They
hadn't been used since 1962 and no judge would ever convict anyone for it, but
they felt it was important. They're also fighting an ever-losing battle to
maintain strict laws concerning the day of the Sabbath (i.e. force everyone to
work as little as possible on Sundays). Their website is literally "closed" on
Sundays.
These things may seem like somewhat insignificant token policies, but from the
perspective of SGP voters they've already lost so much, and they're saving what
they can.
Alienated people tend to, well, seek out other people who are alienated like
them. People who would previously just vote SGP might now become a member. (The
biggest increase in SGP membership? In 1999/2000, when all those liberal gay
marriage, euthanasia, etc. laws were being passed.)