Electrical – Can a USB Oscilloscope be used reliably and accurately for RF projects

The distorted square wave signal (something like the top trace?) is due to a mismatch between your probe's capacitance and the scope's input's capacitance. Your probe should have a tiny screw-like slot to adjust the capacitance. Turn it until you see a proper square wave.
The low level you see is probably due to the probe being set to its 1:10 position.

The problem is that you are using a MEMS digital accelerometer, and what you are reading is the SCK (serial clock) pin of the serial interface. In order to function, that sensor needs to be interfaced with a microcontroller, that sets it for the sampling frequency, the range and so forth.

So you don't have to expect a square wave with 100Hz frequency, but a fast (depending on the bus bitrate) spike, corresponding to a transmission. Expanding the spike, if the scope is fast enough, you should then see the clock square wave inside the spike.

Moreover, if you don't set the SPI interface correctly, the uC will not generate the clock (the sensor operates in slave mode), and you won't read any value.

If you want to see a 100Hz signal, you could probe the Int pin, which sends an interrupt to the microcontroller every time a measure is available. Then, if you handle the interrupt from the microcontroller properly, you wil see the pulse corresponding to the transmission every 10 ms (100Hz).

But make sure that you're not using motion detection; in that case, only when an acceleration is measured, it will generate the interrupt.

To read the data at the SPI port, the simplest thing is to configure the communication with the sensor; otherwise, it won't send data at all. Then, check if the microcontroller is getting the interrupts and if it's reading the data the sensor gives; you can use a timer to add a timestamp to values and check the frequency they come.

(still WIP)