Yes, they are applicable over the optical connection.
The question is whether or not there is anything to be gained by upsampling and the answer is generally No.
CDs use a 44.1 kHz sampling frequency, so 88.2 is twice oversampling and 176.4 if 4 times oversampling. There are a few different upsampling algorithms that could range from as simple as duplicating every sample for 2x upsampling or quadrupling every sample for 4x upsampling to interpolating (sophisticated guessing) values between samples. Either way it is adding information that didn't previously exist.
Upsampling does shift quantization noise to higher frequencies beyond the range of human hearing (44.1 kHz for 2x and 88.2 kHz for 4x) but you won't hear much if any difference as the Nyquist frequency for 44.1 kHz (22.05 kHz) is already above human hearing. At best the higher frequencies near 20 kHz may sound a teeny bit clearer - assuming you are under age 20 and can hear that high anyway. [The vast majority of adults can't hear much at all beyond 16 kHz).