lulu's comment, which focuses on the fact that each of the Stars and Bars solutions are not equally probable, directly answers the original poster's question.
How then should the original math problem be attacked?
To the best of my knowledge, there are (in general) only two means of attack:
Statistical Inference
I don't really know anything about statistics, other than that it was designed to quickly resolve problems of this nature, and yield a reasonable approximation for $~N.~$
I think that someone knowledgeable in statistics should provide a separate answer.
Inclusion Exclusion
This approach, while somewhat convoluted, may be routinely implemented with computer assistance, so that the exact value of $~N~$ may be found. The procedure is laid out below.
Let $~f(N)~$ denote the probability, as a function of $~N,~$ that each of the cookies has at least one chip. Clearly, for $~N < 100, ~f(N) = 0.$
Then, you are looking for the smallest positive integer $~N,~$ such that $~f(N) \geq 0.90.$
So, the entire problem reduces to finding a closed form formula for $~f(N).$
See this article for an
introduction to Inclusion-Exclusion.
Then, see this answer for an explanation of and justification for the Inclusion-Exclusion formula.
Following the syntax in the second link, let $~S~$ denote the collection of all distributions of the $~N~$ chips among the $~100~$ cookies, without any regard for whether each of the cookies has at least one chip.
For $~k \in \{1,2,\cdots,100\},~$ let $~S_k~$ denote the subset of $~S~$ where Cookie-$k$ is in violation, because Cookie-$k$ has no chip.
To clarify, $~S_1~$ denotes the subset of all distributions of the $~N~$ chips among the $~100~$ cookies, where:
Then, with $~N~$ presumed to be a fixed constant, you have that
$$f(N) = \frac{| ~S ~| - | ~S_1 ~\cup ~S_2 ~\cup ~\cdots ~\cup S_{100} ~|}{| ~S ~|}. \tag1 $$
Let $~T_0~$ denote $~| ~S ~|.~$
Let $~T_1~$ denote $~\displaystyle \sum_{1 \leq i_1 \leq 100} | ~S_{i_1} ~|.$
That is $~T_1~$ denotes the sum of $~\displaystyle \binom{100}{1}~$ terms.
Similarly, for $~r \in \{2,3,\cdots,100\},~$
let $~T_r~$ denote $~\displaystyle \sum_{1 \leq i_1 < i_2 < \cdots < i_r \leq 100} | ~S_{i_1} ~\cap ~S_{i_2} ~\cap ~\cdots ~\cap ~S_{i_r} ~|.$
That is $~T_r~$ denotes the sum of $~\displaystyle \binom{100}{r}~$ terms.
Then, by Inclusion-Exclusion theory, $~f(N),~$ which is expressed in (1) above, is equivalent to:
$$f(N) = \sum_{r=0}^{100} (-1)^r T_r. \tag2 $$
So, the entire problem is reduced to finding a closed form formula for $~T_r,~$ as a function of both $~N~$ and $~r.$
Considerations of symmetry greatly simplify the computations.
$$| ~S ~| = T_0 = 100^N.$$
$$T_1 = \binom{100}{1} (100 - 1)^N.$$
Similarly, for $~r \in \{2,3,\cdots,100\}:$
$$T_r = \binom{100}{r} (100 - r)^N.$$
In summary, you are looking for the smallest positive integer $~N,~$ such that the following expression is $~\geq 0.90$:
$$f(N) = \frac{1}{100^N} \times \left\{ ~\sum_{r=0}^{100} ~\left[(-1)^r ~\binom{100}{r} ~(100-r)^N ~\right] ~\right\}. \tag3$$
It becomes a simple matter to write a computer program that will compute $~f(N),~$ and then use the computer program to manually do a numeric search. For example, compute $~f(150).$
Assuming that $~f(150) \geq 0.90,~$ you would then compute $~f(125),~$ and so forth.
$\underline{\text{Addendum}}$
Defects in the above approach:
First see the comment of Henry, immediately following my answer.
Beyond that, my approach assumes that the assignment of each of the $~N~$ chips to one of the cookies are independent events.
In physical reality, this can't be correct, because the volume of the chip is not trivial versus the volume of the cookie. So, in the baking process, as the number of chips assigned to one unit of cookie dough increases, it becomes more difficult than normal to assign an additional chip to that cookie dough unit.
In effect, the chips are (potentially) colliding with each other and crowding each other.
So, one would expect that in an actual baking process, the true value of $~N~$ will be less than the value of $~N~$ computed by my algorithm.
As a different complicating factor, assigning chips to a cookie is different from assigning chips to a unit of cookie dough. That is, since the volume of the cookie is fixed, the more chips that are assigned to a specific cookie, the less cookie dough will be assigned to that cookie.