The suggestion I thought of while reading this thread is to add a percent penalty to units' boarding attempts equal to the square root of current shield strength, applied after all other calculations. That's a simple enough rule and it'd mean that shields would help somewhat in boarding combat but wouldn't completely prevent it unless your shields were 10,000 or more. A tiny shield or a shield that had just started to recharge would have negligible effects on boarding, but a large undamaged shield would become quite dangerous to boarders, and more so as tech increased. Killing a significant percentage of a boarding party with a shield before combat begins could have a disproportionate effect on the subsequent combat, too. And having a policy of boarding ships with full shields could cause serious attrition among your marines in an extended campaign even if they were otherwise able to board ships and defeat crews without taking casualties.
Another solution would be to make it so that when a ship attempts to board a shielded ship, both ships take a hit equal to (HS of boarding ship / HS of target ship, if that's less than 1) * the target ship's current shield strength with the same damage gradient as ramming. Small heavily armored assault shuttles might be able to punch through a strong, intact shield but they'd probably take shock damage, it'd be very dangerous. A ship that had lost its shields and only recovered a few points, though, would barely scratch the paint on a boarding ship with its shields. And if the boarding ship has stronger shields than the boarded ship they'd be able to just absorb the hit. I think something like that hull size comparison needs to be there though, so that a tiny ship can't sacrifice itself to completely negate a huge ship's shields.
Maybe even add both of those to make boarding well-shielded ships technically possible but especially difficult and dramatic. Imagine you're a space marine sent in to board a strongly shielded enemy battleship, the first assault shuttle to go in explodes against the target's shield with the loss of all hands, but then your assault shuttle rams through with heavy damage, losing one of its troop transport bays along with half your company, and then as it maneuvers alongside the target and you cross through space to the hull, a third of your company's remaining marines along with the CO stray too close to an active shield projector and are boiled alive in their power armor. Then when you finally breach the hull, you're badly outnumbered against the crew. As your position is being overrun you think 'this mission would have been a cakewalk if only the shields had been down.' Because boarding almost ignores heavy armor it's good for balance if shields are a good defense against boarding tactics, but instead of making them absolutely negate boarding attempts, it'd be more fun if they made them likely to end in disaster.
Either way, I think boarding being totally prevented by even a single point of shields would just make boarding all but impossible in practice due to shield recharge, and having a certain minimum percentage of shield strength remaining prevent boarding would incentivize adding tiny shields on ships and result in similar problems. If shields affect boarding they should do so according to their objective strength rather than comparing their current strength to their theoretical full strength.
