Actually, Jones and Brown do show up in a very brief shot during the restaurant scene, suggesting they were in fact helping Smith ensure the meeting with Cypher went well, if only as observers.
They're standing behind glass windows in what appears to be a darkened room just beyond the dining area, watching Smith speak with Cypher. The shot occurs directly after Cypher's "ignorance is bliss" line, when the harpist plucks at her strings. However, due to the speed at which the shot then cuts to a close-up on Smith, it's incredibly easy to miss.
- at :0:57 in the video
To answer your question: Smith is conducting business as usual. He hasn't let his façade drop in Cypher's presence because Cypher has yet to prove himself useful regarding the obtaining of Zion's mainframe codes via Morpheus.
It's implied at the beginning of the movie that the Agents had to test Cypher's veracity before they would be willing to work with him. Agent Brown's line to Smith, "The informant is real," is confirmed by Smith's, "Yes." In this case, "the informant" would be Cypher, who had his call to Trinity bugged.