I take it you're adding lemon juice in addition to the normal amount of water you normally use?
If so, yes, you need to reduce the water based liquid so the TOTAL amount of water-based liquid is the correct amount. This is the way to handle adding any water-based liquid, not just lemon juice.
For example, if I use beer to make soap, the total amount of plain water + beer should equal the total amount of water called for by the recipe.
The citric acid in the lemon juice will react with NaOH, so you need to also add extra NaOH to compensate for this neutralization reaction. If you don't, you will be increasing the superfat of the soap. More:
Citric acid, Citrus juice | Soapy Stuff
There is no benefit to adding lemon juice or other acid at trace or at the end of the hot process cook versus at the beginning of soap making. The citric acid in the juice will consume some of the NaOH regardless of when the acid is added to the soap. Adding it sooner or adding it later -- it makes no difference. More:
Acids in soap | Soapy Stuff
The usual reasoning behind adding acid to soap that's intended to wash hair is supposedly adding acid up front will eliminate the need to do an acid rinse after washing the hair. It doesn't work that way. The acid is neutralized in the soap, so it doesn't function as an acid anymore.