So I can provide some clarification and a workaround

Clarification

First off, this only triggers on the EndPackage:

For example, this still allows ggg to autocomplete:

BeginPackage["foo`a`"];
ggg::usage = "asdasd";
EndPackage[];

(*Break this into different cells or the FE acts like EndPackage was called!*)
Abort[]

BeginPackage["foo`", {"foo`a`"}];

But the moment you call EndPackage[] ggg stops autocompleting.

Further investigation shows that even simply messing with the $ContextPath is enough to do it.

BeginPackage["foo`a`"];
ggg::usage = "asdasd";
EndPackage[];

(* again, split these into two cells *)

PrependTo[$ContextPath, "foo`"];

Next, this does not seem to have to do with the standard way the FE handles autocompletions (as I know it at least).

I say this because the following doesn't prevent it from auto-completing (working from a Quit kernel):

BeginPackage["foo`a`"];
ggg::usage = "asdasd";
EndPackage[];

FrontEndExecute@
 FrontEnd`UpdateKernelSymbolContexts[
  "foo`",
  Join[
   {"foo`", "foo`a`"},
   $ContextPath
   ],
  {{"foo`", {"aaa"}, {}, {"aaa"}, {}}}
  ]

And even more to the point, this isn't enough to preserve the autocompletion:

BeginPackage["foo`a`"];
ggg::usage = "asdasd";
EndPackage[];

(* Split the cell here *)

Internal`SymbolList[False]

(* And further split here *)

BeginPackage["foo`"]; EndPackage[]

(* Make sure to call Internal`SymbolList[True] after trying this *)

why this happens is something I haven't been able to figure out. This behavior is a lot like the behavior involved in developerFunctions.m. There doesn't seem to be anything in NeedCurrentFrontEndSymbolsPacket to explain it.

Workaround

Since this triggers on $ContextPath edits, you simply need to edit the $ContextPath again.

This will recover the auto-completion:

BeginPackage["foo`a`"];
EndPackage[];

So after you load your packages, you can use that to get your autocompletions back.