Hi, After getting on the bus at Shiqiao Station how long it will take arrive at Lotus Hill in Guangzhou?

It takes around 40min.

Which way by bus would be shorter: from Shiqiao station (line 3) or Shiqi station (line 4)?
How frequent are these buses? When is the last bus to return from the Lotus Hill?

From Shiqiao Station, you can walk to Danshanqiao Station to take the bus Line Fanyu 92 towards Asian Games' Culture Park to reach Lotus Hill Station and then walk to the entrrance.

From Metro #4, Shiqi station, bus #92 and 93 heads to Lotus Hill. Trip is around 15 minutes, flat rate 2 RMB/person. I would recommend this way to get there compared to Metro #3 and Shiqiao.
(It took us 2 hours by bus, since it was not so easy to find or ask for any bus if you do not speak Mandarin... From Metro #3/Shiqiao, you need to combine bus #1 and #160 or #93, and get support from friendly people...)