I did a shower in Hardieboard sealed with two layers of Redgard. Should I still seal the grout lines even though we used Redgard underneath?
You don't have to. It is completely up to you. Sealing the grout is doing absolutely nothing as far as water-proofing your current setup. I Redgard/HB many showers/tubs and here is what I do:
unsanded - gets sealant. In my opinion it stains easily, especially below level where water constantly hits.
sanded - don't seal it. It looks better unsealed and this grout allows you to "sand" out a stain.
epoxy - no sealant of course.
I always seal the grout, whether or not I'm after one of Custom Building Products' warranties:
A complete CUSTOM Shower Installation System of products must be used including Shower Slope, Shower Base, ANSI A118.4 Bedding Mortar, Sealant, and suitable CUSTOM RedGard Waterproofing and Crack Prevention Membrane to qualify for this limited warranty. –CBP
(I've no affiliation with CBP. If other companies offer similar warranties, I'd love to know about them.)