Does the Geth Pulse Rifle retain its bonus shield damage effect?
The general consensus on the Bioware forum seems to be that this weapon is not worth too much of your attention. There stands to be someone out there who will make a good build around it by using it as a sniper rifle and taking headshot bonuses with an upgrade ammo power (incendiary with headshot bonus perhaps) though.
It does still rip through shields but is highly ineffective against health and armour comparably speaking. Since there are a good deal fewer shielded enemies in ME3 than ME2, the bonus isn't considered to be particularly useful.
There are suggestions that it might be more effective when used in conjunction with ammo upgrades, but overall it's still not the best choice (actually some commenters refer to it as the worst weapon in the game).