The Canon 200D is a good all rounder with the dual pixel AF, but

only has 9 AF points where as the Nikon D5600 has 39. Is this a
deal breaker?

If it was, nobody would have bought Canon entry-level DSLRs for a

long time, as they have had the same diamond-shaped, 9 point
autofocus layout for many years now.

Is it worth getting the Nikon D5600 for an extra $100-200?

That entirely depends on your use-case.

In-depth:

Note that everything below is written without considering both the

200D or the D5600 specifically. This is not meant as a rant against
either manufacturer, but as general information about what one
would look for in a decent AF system.

AF-points (and how much of them are available) is only one aspect
of the whole autofocus-system. I'd even go as far as to completely
ignore the number of AF-points and say that the most important
factors* (in descending order) are:

Focus speed and reliability: A no-brainer, really. If the AF

system takes longer to focus than my subjects bear to hold still,
then it is useless to me. The same applies if it only manages to
get 1/10 - technically well-made - shots in focus. With DSLRs,
that's usually no problem - and if it is, it usually comes down to
the lens.
Low-light-ability: If your camera has 100 AF-points, but only 1
works at moonlight-levels, then when shooting at moonlight-
levels, your camera practically has only 1 AF-point. If you plan
on working with natural light (and/or the lack of it) only, then
this is crucial.
Coverage of the frame: 100 points that would only cover the
innermost 10% of your camera's frame would not be a real
advantage over having 1 (or 5) points in there. Covering a
larger area of the frame will reduce the need to recompose
(meaning: focus your shot via the center AF point, then
subsequently frame your shot (and shoot)).
Distance between the points: The less distance there is
between two AF points, the less I have to recompose (but the
more I have to change my AF-points - or the AF-point matrix).
However, the AF-points you can see in the viewfinder do not
cover the whole area the assigned sensor will work at -
shooting "in between" AF-points therefore will not lead to
misfocussed photos most of the time.
AF-matrices: When shooting shot-critical things (sports,
mainly), having the ability to chose areas instead of single
points of the whole AF-field can make a difference.
Ergonomics: As the density of AF-points increases, if you plan
on using them, a fast way to do so is crucial. With DSLRs, that
usually is no problem, but I would certainly test it before I buy
one.
Ability to deal with high f-numbers: As far as I know, Canon
entry-level DSLRs' AF-systems can deal with up to f/5.6 (I do
not know about Nikon, but I would think that it's about the
same). So if you buy a 70-200mm f/4 L IS II and
an Extender EF 2x III , your effective aperture would
be f/8 - and your AF system would work no more. Also, for
 high apertures, it is not unusual that only the central AF-point
will continue to work.
Cross-type sensors: In my experience, they are somewhat
overrated. I never, ever got a better focus out of the cross-type
sensors of any camera - though I have to admit that I like to
use them for peace of mind.
* "Most important factors" in my opinion - all of them are important, though different
styles of photography will require different features. So, please, don't see this as a
general law of photography. All but the first two can be balanced out by using
some decent technique.

If you want further reading, I recommend Canon EOS DSLR

Autofocus Explained (most of it is not Canon-specific ;-) ).

Conclusion:

The number alone does not account for anything and both cameras
will be quite nice to start your DSLR-career. If I were in your
situation, I would try out both and see which one suits your needs
best. Both systems have their pros and cons (ergonomics, lenses &
flashes, relatives & friends that might lend you lenses & flashes, ...),
and I would consider those, too.

share edited Jan 3 '18 at 3:01 answered Jan 3 '18 at 1:00

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