@gloriouscow
Not an expert but tried to do some sleuthing.
The Vic-II chip datasheet http://cini.classiccmp.org/pdf/Commodore/ds_6567.pdf doesn't say anything special about the light pen input, so I would expect it to be a logic level input. Input high level 2.0 volts minimum.
Does the commodore 64 PCB amplify the signal? https://www.zimmers.net/anonftp/pub/cbm/schematics/computers/c64/250469-rev.A.pdf No, not that I can find. On page 3 in grid E3/4 a series inductor L3 is shown, without a value.
https://www.c64-wiki.com/wiki/Light_pen shows a typical schematic of a light pen. The light sensing device functions as a PNP transistor. (It's shown upside down in that diagram compared to a typical schematic! And the connections are unlabeled. Ugh. 6 is "button1", 7 is +5V and 8 is gnd) When it is DARK, the transistor does not conduct, so the pull up R1 produces a voltage of close to +5V.
When it is illuminated, the light produces a base current and conduction occurs. In this case, the voltage should drop to close to 0V.
Since you are seeing low voltages but not high voltages, check that the pull-up is present and has a plausible value; and that +5V is present.