This topic deserves a book, and it's late and I'm running out of steam, so forgive a ramble.
Metering is a can of worms. Add filtration and it gets worse. Each problematic individually, and the sum more so. Meter through the filter and you have more complexity yet. There's several things I just don't trust involved, and the sum is too shakey to stake my time and film on.
I really don't trust the spectral sensitivity of the meter. Is it full spectrum and matched to my film?
I really don't trust aiming the meter at strongly colored subjects since I have no idea what the meter really sees.
I don't completely trust that I know the spectral response of the film. Which style sensitization am I using?
I don't completely trust the filter factor. It is a numeric compromise averaged for an arbitrary ordinary film response.
I don't completely trust the spectral composition of the incedent light. What color light an I dealing with?
But, what do I trust? I trust that, if the meter is any good at all, it's response to white or neutral light will be roughly proportionate to the film's response. That's about all I trust.
I know some folks meter through the filter and they report it works for them, but... I think they are taking chances. I urge that you do not do so with any of the stronger filters; 15, 21, 23, 25, 29, 47, 58, 61 etc. I won't do it with any filter that has an appreciable influence on color balance.
To hack through the thicket of questions this brings up for me, I meter the least color saturated parts of the scene, wherever that's practical. I only really trust aiming the meter at neutrals, whites, grays and blacks, and take readings aimed at strong colors with a large grain of salt. When I have the time to do it right, I really trust incedent readings, adjusted for the subject at hand by added reflected readings.
I don't trust that the meter will see the same as the film. The only way it is really trustworthy is if you know the meter's sensor has the same spectral sensitivity as the film you are using. Since various films, B&W and color have differing spectral response, there is no way the meter cell matches differing pan emulsions, so that's a poor bet.
Which film is the meter matched to? Plain vanilla panchromatic film? Extended red sensitivity film? An older pan film with less red response? Or a more idiosyncratic response? If I remember correctly, the old Pentax Spot Meter when modified by Zone V! had a filter added to adapt it's response more accurately to their presumptive average film response.
I'm sure this is one more area that could be reduced to numerical exactitude with enough testing and a hand held computer with spreadsheets, but there soon comes a point of diminishing returns for me where testing is involved. So I draw the line here: I meter neutrals in the subject where possible, and the incedent light, with no filter over the meter and add a filter factor later, adjusted as mentioned by previous posters for the light at hand.
C