You shouldn't look at these only as absolute values but rather also at the relative differences. For the player who is on target with every shot (and I accept that will not always be the case so the discrete nature of the damage delivery will have some relevance), we see the following (using your figures):
UT secondary shock : 100%
UT2kx secondary shock: 82%
UT3 secondary shock: 100%
If you factor in the rate of fire and assume a constant fire rate the the damage effect ratio is:
UT3 secondary shock : 100%
UT2kx secondary shock: 80%
I don't think that can be characterised as "not much stronger". Would you describe only getting 80% of your normal pay as "not much of a pay cut"?
Similar considerations apply to the other numbers that you have quoted - you need to look at the relative values
as well as the absolute values.
I'm assuming for the sake of the argument that there is no significant (my definition of significant

difference in the accuracies of given weapons between the games - if there were then that would also have to be factored in when calculating the relative strength of the weapons.
As a package, I'd take UT3's weapons over those of UT2004 any day of the week but that's me.