Yes, and if they had larger mass budgets they could over-engineer things like shield thickness to have wider safety margins, and mitigate unexpected problems like this one. One can speculate future space probes generally will become more more reliable, as the the cost of mass-to-orbit goes down, and engineering constraints become looser.
(I wonder if Starship is useful for this type of problem: if you could adapt the orbital-refueling method to serve as radiation shielding, and put an electronics vault in the middle of the propellant tank? Could you adapt Starship into a spacecraft bus in this way?)
Water tanks are the most likely source of radiation shielding: propellant tanks get used up and go empty, while for any lengthy mission, water is either going to be recycled back into the tanks or you will have to take blue water tanks and over time turn them into grey water tanks, either way you will have those tanks much more filled than the propellant.
These spacecraft always have tons of instruments for measurings along loads of different axes. For example, a magnetometer specifically designed for testing a hypothesis about Europa's magnetosphere. Looking at the wikipedia page it seems like there are about a dozen of these. Perhaps worst case scenario they could determine which one was least critical relative to its weight and eliminate it to increase the mass budget.
(I wonder if Starship is useful for this type of problem: if you could adapt the orbital-refueling method to serve as radiation shielding, and put an electronics vault in the middle of the propellant tank? Could you adapt Starship into a spacecraft bus in this way?)