1. can的反意疑问句一般要分两种情况来说。
2. can如果是表示“能力/许可/请求”等时，则直接以can来变即可。
如你的例子：He can't go to school today, can he?
例句中的can表示的就是能力的含义。
3. can如果表示可能性”，即翻译成“可能/不可能”，则与can无关，必须考查句子的具体时态和谓语动词形式，进行具体判断。
如你的第2/3个例子，can就是表示可能性的含义。
1）He can't work here now,does he?
翻译：他现在不可能在这儿工作，是吗？
方法：去掉can后，结合时间状语now，则句子正常写法为：
He doesn't work here now, does he?
2) He can't have done his work last night，did he?
翻译：昨晚他不可能做过他的工作，是吗？
方法：去掉can后，结合时间状语last night，则句子正常写法为：
He didn't do his work last night, did he?
4. 如果上述情况中没有明确的时间状语，则根据句意可以加以适当变化。
如：He can't have been to the USA before, has he?
方法：去掉can，考虑到时间状语before，用现在完成时最好，即句子改成：
He hasn't been to the USA before, has he?
但是楼主给的第4个例句：
He can't have done his work, did he?/has he?
之所以是两种都可以，是因为去掉can后，没有具体明确的时间状语，所以句子可能变成：
1）He didn't do his work, did he?
也可能变成：
2）He hasn't done his work, has he?
参考资料：原创回答团(159号会员)