I am not seeing this behavior (in 10.0.1, on Linux). I can say that, generally speaking, when all definitions have been cleared it is an indication that the kernel has crashed.

I'm not sure that I understand your "bug", but the last two lines do execute on my machine (10.0.1 in Windows 7 64 bit).

In[1]:= $Messages=.
In[2]:= Clear[sp1900,sp1900d]
sp1900=Table[i,{i,1,8000}];
sp1900d=Module[{t},t=Sort[sp1900];Table[{t[[i]],Length[t]-i+1},{i,1,Length[t]}]];
In[5]:= Clear[sp1900dsc,sp1900sc]
sp1900dsc=Drop[sp1900d,0] ;
sp1900sc=Drop[sp1900,0] ;
In[8]:= sp1900sc[[1]]
sp1900sc[[Length[sp1900sc]]]
Out[8]= 1
Out[9]= 8000

With the new version 10.0.2 of Mathematica this issue seems to have been solved. Thanks to the people of Wolfram Research!