There are definitely situations in materials science and mechanical engineering when jerk is more important than acceleration as a factor in causing damage. A term I've seen used is "load rate." This can refer to either $dF/dt$ or $da/dt$, which differ by a factor of $m$. You'll see the acronyms ALR and ILR for average and instantaneous load rate.
A steady force can't cause wave excitations, but a varying force can. For example, when you're machining something on a mill or lathe, jerk produces "chitter," which can spoil your work. Engineers designing cams work very hard to minimize the jerk of the cam follower: "Remember also that jerk translates to an impulse and excessive impact ultimately leads to scuffed and pitted cam follower." (Blair 2005)
I know of a couple of good examples involving the human body. In crewed spaceflight, astronauts are exposed during a launch not just to high accelerations but also sometimes to what's known as a "pogo," which means an oscillating acceleration in the longitudinal direction. A pogo with an amplitude as small as $0.5g$ can apparently cause extremely unpleasant sensations in the eyeballs and testicles, as well as heating of the brain and viscera (Seedhouse 2013). Heating is a phenomenon you can't get from a static force.
Another human-body example involves running injuries. Measurements using accelerometers attached to runners' feet, legs, or hips show that during a stride cycle, there are typically two different peaks, an impact peak and another "active" peak that occurs during propulsion. The impact peak has a smaller acceleration but a larger jerk, and seems to be the factor that causes injuries: "increased impact loading was associated with an elevated risk of sustaining a running injury while peak vertical force was not." (Davis 2010)
G. P. Blair, C. D. McCartan, H. Hermann, "The Right Lift", Race Engine Technology, Vol. 3 lssue 1, August 2005
Irene Davis, quoted in http://lowerextremityreview.com/news/in-the-moment-sports-medicine/impacts-spell-injury , 2010
Erik Seedhouse, 2013, Pulling G: Human Responses to High and Low Gravity
There are various ways of calculating acceleration and jerk from your data set.
The value of $\mathrm{d}t$ you want is the time step generally, in your case $100 \, \mathrm{ms}.$
The method that you suggest
$$a=\frac{v_2-v_1}{\mathrm{d}t}$$
will give you an answer and is reasonable, but it will not give you the best value I expect. It might be better to use something like Savitsky-Golay fitting of the data set, which you can do to get derivatives.
The formula you suggest can be used for jerk, just put in two accelerations instead of two velocities. The only problem with this is that at each step you are getting further and further from the data, so any experimental errors in position will get magnified in each step of calculation for velocity, acceleration and the worst would be jerk.
I would be tempted to use two different methods and finding velocity (+ acceleration and jerk if possible) and then compare the velocities from different methods and it may give an indication of how reliable your analysis is.
The Wikipedia page on Savitsky-Golay fitting has parameters for finding 1st 2nd 3rd... derivatives at the bottom.
Note that in reply to your question I would draw up a table in each dimension like this:
$$
\begin{array}{c|c|c|c|c}
\text{time,}~t & \text{position,}~x & v=\frac{\mathrm{d}x}{\mathrm{d}t} & a=\frac{\mathrm{d}^2x}{{\mathrm{d}t}^2} & \text{jerk}=\frac{\mathrm{d}^3x}{{\mathrm{d}t}^3} \\ \hline
0 & 0 & 10 & 5 & 4 \\
1 & 10 & 15 & 9 & 3 \\
2 & 25 & 24 & 12 & 2 \\
3 & 49 & 36 & 14 & 1 \\
4 & 85 & 50 & 15 & \vdots \\
5 & 135 & 65 & \vdots \\
6 & 200 & \vdots \\
\vdots & \vdots
\end{array}_{\Large{.}}
$$
Hope this is helpful – of course the velocities should have times in between the times for $x$ and the accelerations times between the times of the velocities etc. etc. – but it is not so easy to figure out how to indicate that in a table in an answer here.
Best Answer
Yes, since the acceleration and jerk are both vector quantities, your equations should be ok.