According to many sources, Alexandra had difficult pregnancies and had large babies (8+ lb babies; some writers have suggested gestational diabetes, though that'll obviously never be proven), as well as her chronic sciatica progressively getting worse over time. Also, when Alexis was born, Alix was thirty-two, considered an advanced maternal age for the day. It was probably a decision made between Nicholas and Alix to not further aggravate her physical health. Anyone that reads up on Romanov history realizes the psychological effect of Alexis' diagnosis on her in the years following.

I would imagine that, knowing that hemophilia was genetic (even with the limited/lack of knowledge of the variants of hemophilia of the day, they knew that), they made the decision to not chance it again - a couple of writers have speculated on it, but again, not provable.

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Robert Massie's book "Nicholas and Alexandra" explores the effects of hemophilia on them - he became interested in them because his own son was a hemophiliac. Even though it's 40 years old, it's still a good read and a good place to start.

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Edit: spelling, wording