Besides the practicalities of crystals themselves, there is also the matter of the logic interface. To be clear, silicon oscillators are also available with crystal-level stability, and in high frequencies. Why not use them?
Well, cost for one; they might not be as cheap as quartz or other resonator based oscillators. But besides that, too:
Most MCUs work with CMOS logic levels, at relatively high supply voltages (3.3+ V). Every switching edge must push the capacitance of its pin driver, the connecting trace, and the receiving pin, more or less fully from rail to rail. At low frequencies, this is fine, but as frequency goes up, rise time must get faster and faster to maintain low jitter, and the power consumption of all that voltage swing keeps going up.
For example, a 10 pF pin plus trace capacitance (which is probably fairly typical, or maybe on the low side, for a typical short distance between oscillator and MCU, and their typical pins), dissipates E=12CV2 or 55 pJ per switching edge. At 10 MHz, this is 550 µW, not a big deal in the grand scheme of things, but definitely an annoyance for a battery-operated device, say. And at 100 MHz, it's 5.5 mW. Still hardly going to start a heat wave, but it also adds up quickly when compared with the power-efficient on-chip logic (that might be running at 1.2 V even, and is made from truly microscopic transistors with nearly negligible capacitances). Meanwhile, you've got traces on the board that are making electrically-short antennas, and driving a couple volts into them at 100 MHz or whatever means you're going to get, not a great amount of radiation, maybe it's -40 dB gain or whatever — but when your limit is -60 dBµV say, now you're over the limit by the ballpark of say +20 dB!
At still higher frequencies, power consumption and EMI become burdensome, and LVDS or ECL signaling becomes more efficient. These use a small current or voltage swing, thus incurring less power dissipation pushing around capacitances, and are matched-impedance (which, actually, we're not pushing around capacitance at all anymore, or not primarily anyway, but rather the characteristic impedance of a transmission line — meanwhile, edge rates are fast enough that transmission line behavior is relevant to signal quality analysis, even for fairly short runs). Meanwhile, particularly for differential (LVDS, etc.), the complementary traces mean radiation is largely canceled out, except very near the traces, or if the run ends up unbalanced (length matching is important, as is avoiding nearby traces / floating copper / etc. which can couple to one trace more than the other and increase radiation).
Alternately, we could remove the square wave harmonics so we don't have to switch fully back and forth all the time — indeed, we can go further and use a resonant circuit to null out the pin/trace reactance and pass around a high-frequency sine wave with almost arbitrarily low power consumption. But this makes the transmitter and receiver much more complicated: the transmitter must be internally filtered and able to supply continuous analog levels; and the receiver needs a comparator to recover sharp digital edges, or an RF mixer based PLL to use the sine wave directly. And needless to say, we lose the nice property of digital logic (trace length ~doesn't matter, at worst we only need to worry about source and/or load termination resistances) and suddenly need a ton of finicky tuning reactances on the board.
That said, sine-wave oscillators are available, too. There are indeed sine-input PLLs, or if you're working with a radio system, the sine might be used directly by a mixer.