This type of datapoint is actually very helpful for estimating the variance
This is quite unsurprising when you think a bit more about it. Just as it is a very different thing to estimate a mean and a variance, estimating the slope of a line is a very different thing to estimating the variance of a deviation of values around that line. It is possible for information to be very helpful in estimating the mean of a distribution and very unhelpful in estimating its variance, or vice versa.
A datapoint at $x_i=0$ cannot affect the slope estimate because it tells you nothing about the behaviour of the true regression line that you don't already know from the fact that it passes through the origin. For this datapoint the deviation $y_i \neq 0$ must be pure "error" that is not attributable to the regression, so it does not contribute to the slope estimator. However, it is precisely because it represents error (i.e., deviation from the true regression line) that this point does give you information about the error variance in the regression, and therefore about the variance of the slope estimator.
As a thought experiment to confirm this intuition, imagine that you only had one datapoint with $x_i \neq 0$, so that your estimated slope would just be the slope of the line through the origin and that single point (which we will here call the "slope-informative point"). Now, imagine that all your other datapoints fall at $x_i = 0$. If these non-slope-informative datapoints are all tightly packed around $y_i \approx 0$ then that tells you that the error variance in the model is low, which means that the error variance for the slope-informative point is low, which means that the true regression value at that point is close to the observed value. Naturally, this will mean that your estimated slope is more accurate and your confidence interval for the true value of the slope will be narrow. Contrarily, if those non-slope-informative datapoints are all large deviations from zero (i.e., $|y_i| \gg 0$) then that tells you that the error variance in the model is high, which means that the error variance for the slope-informative point is high, which means that the true regression value at that point is potentially far away from the observed value. Naturally, this will mean that your estimated slope is less accurate and your confidence interval for the true value of the slope will be wide.