You had better bet that General Lee new exactly how many effectives he had. And I do believe what he says. Under 40,000.
It is a heart breaking thought of all those men to0 feeble to follow him where he led them.
No he didn't. He sent the circular on the 12th precisely because he didn't know the strength of his army. They hadn't stopped to count the men since well before 2nd Bull Run. Lee believed he was going to attack McClellan with his large army (ca. 87,000 effectives before 2nd Bull Run), and he acted like it. Even after Antietam Lee tried to renew the combat by crossing at Williamsport, which would be insane if he knew he only had ca. 40,000 effectives remaining. However, until after Antietam there is little evidence Lee knew just how weak his army had become. He wrote to his President on the 21st detail what he knew:
"The army is resting to-day on the Opequon, below Martinsburg. Its present efficiency is greatly paralyzed by the loss to its ranks of the numerous stragglers. I have taken every means in my power from the beginning to correct this evil, which has increased instead of diminished. A great many men belonging to the army never entered Maryland at all; many returned after getting there, while others who crossed the river kept aloof. The stream has not lessened since crossing the Potomac, though the cavalry has been constantly employed in endeavoring to arrest it. As illustrative of the fact, I inclose a report(*) just received from General J. R. Jones, who was sent to Winchester to arrest stragglers at that point while the army was at Sharpsburg. It occasions me the greatest concern in the future operations of the army, for it is still my desire to threaten a passage into Maryland, to occupy the enemy on this frontier, and, if my purpose cannot be accomplished, to draw them into the Valley, where I can attack them to advantage. Some immediate legislation, in my opinion, is required, and the most summary punishment should be authorized. It ought to be construed into desertion in face of the enemy, and thus brought under the Rules and Articles of War. To give you an idea of its extent in some brigades, I will mention that, on the morning after the battle of the 17th, General Evans reported to me on the field, where he was holding the front position, that he had but 120 of his brigade present, and that the next brigade to his, that of General Garnett, consisted of but 100 men [in fact this brigade had over 500 at this time]. General Pendleton reported that the brigades of Generals Lawton and Armistead, left to guard the ford at Shepherdstown, together contained but 600 men. This is a woeful condition of affairs, and I am pained to state it, but you ought not to be ignorant of the fact, in order, if possible, that you may apply the proper remedy. It is true that the army has had hard work to perform, long and laborious marches, and large odds to encounter in every conflict, but not greater than were endured by our revolutionary fathers, or than what any army must encounter to be victorious. There are brilliant examples of endurance and valor on the part of those who have had to bear the brunt in the battle and the labor in the field in consequence of this desertion of their comrades. "
All these weak brigades were reported to be weak to Lee after the battle. Lee simply didn't know at the time how weak he was.